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The main goal of Cell Biology is to reveal to the students how the living cell works which will give them the background for the subjects in the upcoming years.
For that, we introduce them to the structure and function of every single compartment of the cell and its chemical composition. Other areas such as cell communication, cell division, and regulation of the cell cycle are studied.
Themes: Structure of prokaryotic and eukaryotic cells, membranes, membrane organelles, DNA and chromosomes, cell communication, cell cycle, reproduction of organisms.
Last update: Svobodová Zuzana, Mgr., Ph.D. (21.08.2024)
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The final exam test is in written form and is composed of 35-40 questions. Types of questions: single best answer, matching, fill in or image description. The limit for passing the test is minimally 70% of correct answers:
If the student regularly studies using the Cell biology course in Moodle, he/she can obtain from 0.5 up to 2.5 bonus points for the final exam test. Last update: Svobodová Zuzana, Mgr., Ph.D. (21.08.2024)
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Obligatory:
Last update: prepocet_literatura.php (19.09.2024)
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Lectures - theory Moodle - videos, "quizzes", "questions and answers", make-up own "glossary" Last update: Svobodová Zuzana, Mgr., Ph.D. (21.08.2024)
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The student should show knowledge across the subject of Cell Biology, specifically in the following areas: 1. Definition and general characteristics of cell 2. Structure of prokaryotic cell 3. Structure of eukaryotic cell 4. Cell nucleus 5. Structure of DNA 6. Chromosome structure in prokaryotes and viruses 7. Chromosome structure in eukaryotes 8. Replication, transcription and translation 9. Structure of living systems – water, inorganic substances, low molecular weight organic molecules (saccharides, organic acids, amino acids, nucleotides, phospholipids) 10. Structure of living systems – high molecular weight organic molecules (polysaccharides, proteins, nucleic acids) 11. Membrane structure 12. Cytoplasmic membrane 13. Membrane transport (carrier proteins, ion channels) 14. Mitochondria (structure, cellular respiration) 15. Chloroplasts (structure, photosynthesis) 16. Endoplasmic reticulum 17. Golgi apparatus 18. Endosomes 19. Lysosomes 20. Peroxisomes 21. Intracellular vesicular transport 22. General principles of cell communications 23. Receptors (basic characteristics, signalling cascade) 24. Ion-channel–coupled receptors 25. G-protein–coupled receptors 26. Enzyme–coupled receptors 27. Microtubules 28. Actin filaments 29. Intermediate filaments 30. Cell cycle 31. Mitosis 32. Meiosis 33. Cell cycle control system 34. Cell differentiation 35. Cell death 36. Cell stress 37. Asexual reproduction 38. Spermatogenesis 39. Oogenesis 40. Fertilization Last update: Svobodová Zuzana, Mgr., Ph.D. (21.08.2024)
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Cell structure · definition and general characteristics of a cell (cell theory) · structure of prokaryotic cell · structure of eukaryotic cell (plant and animal)
Chemical composition of living systems · water and inorganic substances · low molecular weight organic molecules: saccharides, organic acids, amino acids, nucleotides, phospholipids · high molecular weight organic molecules: polysaccharides, proteins, nucleic acids
Nucleic acids and chromosomes I · structure of DNA · chromosome structure in prokaryotes and viruses · chromosome structure in eukaryotes
Nucleic acids and chromosomes II · replication · transcription · translation
Membranes I · membrane structure o lipid bilayer o molecular structure of membranes – lipids, proteins, saccharides · cytoplasmic membrane
Membranes II · membrane transport · carrier proteins · ion channels and the electrical properties of membranes
Membrane organelles I · mitochondria o the structure o cellular respiration – Krebs cycle, electron-transport chain, oxidative phosphorylation · chloroplasts o the structure o photosynthesis – light reactions and dark reactions
Membrane organelles II · endoplasmic reticulum · Golgi apparatus · endosomes · lysosomes · peroxisomes · intracellular vesicular transport o transport from the endoplasmic reticulum through the Golgi apparatus o transport from the trans Golgi network to lysosomes o transport into the cell from the plasma membrane: endocytosis o transport from the trans Golgi network to the cell exterior: exocytosis
Cell communications · general principles of cell communication · signal molecules · receptors o ion-channel–coupled receptors o G-protein–coupled receptors o enzyme–coupled receptors
Cell division · cell cycle - four phases (G1, S, G2, M) · mitosis - prophase, prometaphase, metaphase, anaphase, telophase, cytokinesis · meiosis
Cell cycle control system · regulation of the cell cycle · cell differentiation · cell death
Reproduction of organisms
Last update: Svobodová Zuzana, Mgr., Ph.D. (21.08.2024)
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Institution: Charles University, Faculty of Pharmacy in Hradec Králové, Dep. of biological and medical sciences
Lecturers: Dr. Zuzana Svobodová a Dr. Petra Fikrová
Learing outcomes for subject: Cell biology
Topic 1: Cell Structure Syllabus – Cell Structure • Definition and general characteristics of the cell (cell theory) • Structure of prokaryotic cells • Structure of eukaryotic cells (plant and animal) Learning Objective: Students should understand the Cell Theory, the three basic domains of living organisms, and know the structure of prokaryotic, eukaryotic, animal, and plant cells. Knowledge Tasks: • Name the three basic domains of living organisms • Characterize the typical properties of Archaea • What do Archaea have in common with bacteria and eukaryotes? • What is typical for halophilic Archaea? Name one representative • What is typical for methane-producing Archaea? Name one representative • What is typical for hyperthermophilic Archaea? Name one representative • What is typical for Archaea without a cell wall? Name one representative • Name the four basic statements of cell theory • Name the four basic properties common to all cells • Define which cells are classified as prokaryotic and which as eukaryotic • Name the basic structures of eukaryotic cells and describe their functions (4 components of the nucleus, ER, GA, ribosomes, vesicles, vacuole, mitochondria, chloroplast) • Name the basic structures of prokaryotic cells and describe their functions (3 possible envelopes, flagellum, pili, nucleoid, plasmids, ribosomes) • Describe the difference between the nucleoid of a prokaryotic cell and the nucleus of a eukaryotic cell • Describe the difference between the ribosome of a eukaryotic and a prokaryotic cell • Describe what mitochondria and chloroplasts have in common and how they differ • Name the three basic types of cytoskeletal fibers (typical occurrence and function) Topic 2: Chemical Composition of the Cell Syllabus – Chemical Composition of the Cell • Water and inorganic substances • Low-molecular-weight organic substances: carbohydrates, organic acids, amino acids, nucleotides, phospholipids • High-molecular-weight organic substances: polysaccharides, nucleic acids, proteins Learning Objective: Students should know the chemical composition of living systems – water, inorganic substances, low-molecular-weight organic substances (carbohydrates, organic acids, amino acids, nucleotides, phospholipids), and high-molecular-weight organic substances (polysaccharides, proteins, nucleic acids). They should have an overview of the chemical bonds present in these molecules. Knowledge Tasks: • Characterize the basic chemical bonds found in living organisms (covalent non-/polar, ionic, non-covalent bonds) • Describe the typical features of hydrogen bonds in terms of strength and stability. Define between which atoms they form • Name the chemical elements that make up living organisms (macrobiogenic, oligobiogenic, and trace elements) • Explain why water is a liquid and not a gas (under normal temperature and pressure conditions) • Which ions are the main components of extracellular and intracellular fluids • Name what polysaccharides are made of, the type of bond that connects them, and one representative • Name what proteins are made of, the type of bond that connects them, and one representative • Name what lipids are made of, the type of bond that connects them, and one representative • Name what nucleic acids are made of, the type of bond that connects them, and one representative • Define the basic composition of phospholipids and the properties of this molecule • Name at least four representatives of nucleotides, their basic function, composition, and occurrence in the cell • Provide the basic classification of amino acids into four groups, define their properties, and name one representative • Describe the basic structure of a protein (N-terminus, C-terminus, polypeptide backbone, side chains) • Define the basic function of chaperones • Define which parts of the protein and which bonds are involved in the primary, secondary, tertiary, and quaternary structure • Describe what is typical for the secondary structure of a protein, alpha-helix, and beta-sheet • Define what a protein domain is and give an example • Describe which structures or bonds are involved in the interaction of the binding site and the target molecule Topics 3 and 4: DNA and its Structure Syllabus: Nucleic Acids and Chromosomes I • Structure of DNA • Structure of chromosomes in prokaryotes and viruses • Structure of chromosomes in eukaryotes Nucleic Acids and Chromosomes II • Replication • Transcription • Translation Learning Objective: The students should know the structure and form of nucleic acids found in living organisms and viruses. They should know in what form they are found in the chromosomes of organisms. Students will understand how information is encoded in DNA in the form of genes and how DNA replication occurs during cell division. Part of their knowledge should be understanding cell biology's central dogma and its basic transcription and translation processes. Knowledge Tasks: • Describe the composition of nucleotides in DNA and RNA • Name the possible nucleotides found in DNA and RNA • Name the chemical bonds involved in the structure of the DNA double helix and describe the charge characteristics of DNA • Explain what Watson-Crick base pairing means • State how many hydrogen bonds are involved in base pairing in DNA and RNA • Name the enzyme involved in supercoiling • Name the basic types of RNA in the human body and describe their basic functions (3 main types + 1 other, e.g., microRNA) • Provide what ribosomes are made of and describe their life cycle (where they are formed and where they degrade) • Define what a gene is • Name and characterize the three basic types of genes • Describe and give examples of what constitutes genic and non-genic DNA • Define what a genome is and what a genophore is • Name the genophores found in prokaryotic and eukaryotic cells • Describe the occurrence of DNA and RNA in viruses and give examples • Define what a eukaryotic chromosome is made of and which proteins are involved in its structure • Describe the form in which it is found in the interphase chromosome and during mitosis • Describe which parts of the human genome are found in the nucleus as euchromatin and which as heterochromatin • Describe what the nucleolus is made of and its function • Define the following terms: karyotype, homologous chromosomes, non-homologous chromosomes, gonosomes, autosomes • Describe when and how inactivation of one X chromosome occurs in women. Describe the form in which the chromosome is then found • Explain why the replication process is called "semi-conservative" • Explain the terms "replication origin and replication fork" • Provide how many replication origins are found in eukaryotic organisms and how many in prokaryotic organisms • Name the enzymes involved in DNA replication during cell division and briefly describe their function (helicase, DNA polymerase III, I, DNA ligase, primase, topoisomerase I/II, or telomerase) • Explain the term "asymmetry of the replication fork, leading strand, lagging strand, Okazaki fragments" • Explain the following terms "gene expression” and “central dogma of molecular biology". Describe the two basic steps they consist of and briefly describe them • Explain the term "transcription" and identify the target product of this process • Name the enzymes and nucleotides used in transcription • Explain what "primary transcript" means • Describe the three steps of post-transcriptional modification of pre-mRNA • Describe the mechanism of pre-RNA splicing • Explain the terms "genetic code, codon, reading frame" • Learn to use the genetic key to translate mRNA into an amino acid sequence • Describe the structure of tRNA, e.g., where the amino acid is attached, where the anticodon is located, etc. • Explain how tRNA pairs with amino acids • Describe the structure of the ribosome in terms of transcription, where the binding site for mRNA is, where the M/P/E site is • Characterize the three phases of translation (initiation, elongation, and termination) • Describe the differences in gene expression between prokaryotes and eukaryotes Topics 5 and 6: Membranes I and II Syllabus: Membranes I • Structure of membranes o Lipid bilayer o Molecular structure of membranes – lipids, proteins, carbohydrates • Cytoplasmic membrane Membranes II • Transport of substances across membranes • Transport proteins • Ion channels and membrane potential Learning Objective: Teach students the structure and composition of the plasma membrane. Explain the principles of substance transport across the membrane. Students should know the basic types of substance transport through ion channels and transporters. Students will understand the concepts of membrane potential and nerve impulse conduction. Knowledge Tasks: • Name the three basic groups of substances forming the plasma membrane and describe their basic functions in the membrane • Name several representatives from each group • Describe the basic structure of a phospholipid, its properties, and the possibilities of movement within the bilayer • Provide how the composition of phospholipid chains contributes to changes in membrane fluidity and provide an example • Explain the distribution of different types of phospholipids in the membrane and which organelles and enzymes are involved in this arrangement • Describe how the presence of cholesterol affects membrane properties • Define what glycolipids are, where they are located, and their function • Name the four basic functions of proteins in membranes • Describe how proteins are integrated into the membrane • Name the ways proteins can move within the membrane and the ways they can be anchored in the membrane (4) • Describe when and how glycosylation of proteins and lipids occurs • Define what the glycocalyx is and its function • Define what transporters are, describe their structure and function • Name the substances the transporters transport and the types of transport they enable concerning the number of transported substances or energy use • Define osmosis and explains how the water passes through the membrane • Name the types of osmotic phenomena that can occur and how they occur in animal and plant cells • Name three ways cells avoid osmotic swelling • Describe which substances pass through the membrane by diffusion very easily, easily, slowly, or “not-at-all”, and provide specific molecules (2-3) • Define what an electrochemical gradient is and how it affects the rate of passage of charged molecules through the membrane • Define the three types of ATP pumps and the type of molecules they usually transport • Describe the principle of light-driven transport • Explain the principle of glucose-sodium symport, Na+/H+ antiport, Ca2+ pump, sodium-potassium pump (provide the ratio of transported ions) • Define what ion channels are, describe their structure and function • Name the substances ion channels transport and the types of transport they enable concerning the nature of the transported substances or energy use • Name the four types of ion channels and the principles of their regulation • Explain how nerve impulses are conducted • Define what an action potential is (5 steps) • Explain why the action potential propagates in only one direction and what contributes to this • Define what saltatory conduction is • Explain how synaptic (chemical) signal transmission occurs • Which neurotransmitters are excitatory and which are inhibitory (2 examples of each) and describe the principle of the phenomenon Topics 7 and 8: Membrane Organelles I and II Syllabus: Membrane Organelles I • Mitochondria o Structure o Cellular respiration – Krebs cycle, respiratory chain, oxidative phosphorylation • Chloroplasts o Structure o Photosynthesis – light and dark phases Membrane Organelles II • Endoplasmic reticulum • Golgi apparatus • Endosomes • Lysosomes • Peroxisomes • Mechanisms of protein entry into organelles o Transport from the cytosol to the nucleus – nuclear pores o Transport from the cytosol to the ER, mitochondria, chloroplasts, and peroxisomes o Transport from the ER to other compartments Learning Objective: Learn students the structure of mitochondria and chloroplasts. Explain the principles of cellular respiration and photosynthesis. Explain in detail the function of the endomembrane system. Familiarize students with the mechanisms of protein entry into organelles (nucleus, ER, GA, chloroplasts, peroxisomes, and other cell compartments), membranes, or outside the membrane (into the extracellular space), as well as endocytosis of substances from the external environment. Knowledge Tasks: • Describe the basic structure of mitochondria, what the matrix contains, and what processes occur in each part of the mitochondria • Name several representatives from each group • Describe the specifics of mitochondria in germ cells, in muscle, or in liver cells • Name the individual steps of cellular respiration (4), where they occur in the cell, and which substances enter and exit them • Provide the energy balance of the Krebs cycle and the respiratory chain for 1 acetyl-CoA • Name the three complexes forming the respiratory chain in the correct order • Describe the structure and function of these complexes • Explain how the proton gradient in the mitochondria is formed and what it is used for • Explain the principle of ATP synthase • Describe the energy metabolism of the mitochondria in a summary diagram (which substances enter, which exit, and the sequence of steps) • Describe the basic structure of chloroplasts, what the stroma contains, and what processes occur in the chloroplast and where • Define what the light and dark phases of photosynthesis are (which substances enter and leave the process, what is the benefit for organism) • Describe where the antenna and reaction center are located, their structure, and function • Explain the principle of high-energy electron transfer within photosystem I, the cytochrome b and f complex, and photosystem I, and the subsequent formation of the proton gradient associated with ATP production • Describe where the Calvin cycle occurs, which substances enter and exit it • Provide the energy balance of the Calvin cycle • Describe the importance of photosynthesis for the plant and its surroundings • Explain how proteins enter membrane organelles, Name the three main mechanisms • Explain what a signal sequence is, its structure, and which proteins it occurs in • Explain the two populations of ribosomes and which proteins are synthesized on them • Describe the main functions of rough and smooth ER • Explain the principle of protein synthesis on ER ribosomes • Describe the principle of protein integration into the ER membrane according to the diagram • Define the main and side branches of the secretory pathway and the endocytic pathway in vesicular transport • Describe the formation of clathrin-coated vesicles and the molecules involved • Explain the principle of vesicle targeting to target structures (including fusion) and the molecules involved • Explain the regulation of Ca2+ ion concentration in the cytoplasm in relation to muscle contraction • Describe the structure of the GA, explain its basic functioning, and the passage of substances contained in vesicles from the cis side to the trans side of the GA • Explain the principle of the basic and regulated pathways of exocytosis • Explain the forms of the endocytic pathway in pinocytosis, phagocytosis, and autophagy • Describe the structure and function of peroxisomes and lysosomes Topic 9: Communication Between Cells Syllabus – Basic Types of Signaling, Receptors, Chemoreception, Ion Channel-Linked Receptors, G Protein-Coupled Receptors, Enzyme-Linked Receptors Learning Objective: Students will be able to describe different types of cell communication: endocrine, paracrine, neuronal, and contact-dependent signaling. They will be able to explain the differences between surface and intracellular receptors and their roles in cell signaling. Students will understand how different types of receptors (ion channels, G protein-coupled receptors, and enzyme-linked receptors) transmit signals into the cell and how signaling cascades transmit and amplify signals within the cell. Knowledge Tasks: • Define and characterize the basic types of cell signaling: endocrine, paracrine, neuronal, and contact-dependent, and provide an example for each type. • Explain the general role of receptors and intracellular signaling cascades in cell signaling. • Compare the localization and resulting properties of signaling molecules for surface and intracellular receptors and provide an example for each type. • Define and characterize the types of membrane receptors: enzyme-linked receptors, ion channel-linked receptors, G protein-coupled receptors. • Explain the role of G proteins and their components in cell signaling. • Explain the role of second messengers in cell signaling. • Name and characterize the second messengers of enzymes linked to G proteins: adenylate cyclase and phospholipase C. • Describe (or draw a diagram) how protein kinase A is activated. • Describe (or draw a diagram) how protein kinase C is activated.
Topic 10: Cell Division Syllabus – 4 Phases of the Cell Cycle (G1, S, G2, M), Mitosis (Prophase, Prometaphase, Metaphase, Anaphase, Telophase), Cytokinesis, Meiosis Learning Objective: Students will be able to describe the individual phases of the cell cycle and explain the process of mitosis, including its phases, and describe the differences in cytokinesis between animal and plant cells. Additionally, students will be able to describe the process of meiosis and understand the significance of genetic recombination and crossing-over for genetic variability. Knowledge Tasks: • Define and characterize the individual phases of the cell cycle. • Explain the significance and main events that occur in each phase of the cell cycle. • Describe the process of DNA replication and name the enzymes involved, explaining the semi-conservative nature of DNA replication. • Describe the structure of chromosomes and their role in heredity. • Explain the differences between prokaryotic and eukaryotic chromosomes. • Explain the differences between binary fission and mitotic cell division. • Describe the process of mitosis and its phases: prophase, prometaphase, metaphase, anaphase, and telophase. • Explain the role of the mitotic spindle and describe its influence on chromosome movement. • Describe the mechanism and significance of cytokinesis. • Define and explain the differences between cytokinesis in animal and plant cells. • Describe the individual phases of meiosis and explain how the process of meiosis fundamentally differs from mitosis. • Explain the significance of meiosis in sexual reproduction. • Describe in detail the process of recombination (crossing-over) and its significance in genetic diversity. Topic 11: Regulation of the Cell Cycle Syllabus – Cell Cycle Regulation System, Cell Differentiation, Cell Death Learning Objective: Students will be able to describe how the cell cycle is regulated using checkpoints (G1, G2, M) and understand the role of cyclins and cyclin-dependent kinases (Cdks) in cell cycle regulation. Additionally, students will be able to distinguish between different types of cell death - necrosis and apoptosis, including their triggering signals and physiological or pathological significance. Learning Outcomes: • Explain the significance of the four main phases of the cell cycle (G1, S, G2, M) in the context of cell division and growth. • Identify where the main checkpoints of cell cycle regulation are located and what questions the cell answers before proceeding to the next phase. • Explain the importance of checkpoints in ensuring the proper progression of the cell cycle and preventing DNA damage. • Describe how cyclins and Cdks work together to regulate the individual phases of the cell cycle. • Describe the role of Cdk inhibitory proteins in halting the cell cycle in the event of DNA damage. • Provide examples of situations where the cell cycle is halted and how cells repair damaged DNA before continuing the cycle. • Explain the differences between apoptosis (programmed cell death) and necrosis (catastrophic cell death). • Describe the physiological and pathological conditions that lead to apoptosis and its significance for the organism. • Discuss how growth factors and other extracellular signals influence the cell cycle and explain how these signals can stimulate or inhibit cell division. • Describe how dysregulation of the cell cycle can lead to uncontrolled cell division and tumor transformation. • Provide examples of genes that play key roles in cell cycle regulation and tumor suppression. Topic 12: Reproduction of Organisms Syllabus – Asexual Reproduction (Characteristics, Binary Fission, Budding, Fragmentation, Vegetative Reproduction), Sexual Reproduction (Characteristics, Spermatogenesis, Oogenesis, Fertilization) Learning Objective: Students should understand concepts such as asexual and sexual reproduction, binary fission, budding, and fragmentation. They should be able to explain processes such as meiosis, gametogenesis (spermatogenesis and oogenesis), and fertilization, including their significance for genetic diversity. Knowledge Tasks: • Define asexual reproduction and provide examples of organisms that reproduce this way. • Define sexual reproduction and describe its evolutionary significance compared to asexual reproduction. • Explain the principle of binary fission and provide examples of organisms that reproduce this way. • Explain the principle of budding and provide examples of organisms that reproduce this way. • Explain the principle of fragmentation and provide examples of organisms that reproduce this way. • Explain the principle of vegetative reproduction in plants. • Explain how sexual reproduction leads to genetic diversity through the combination of gametes. • Compare the processes of mitosis and meiosis, including their roles in asexual and sexual reproduction. • Describe the process of spermatogenesis and oogenesis and their significance in sexual reproduction. • Describe the process of fertilization, including the roles of sperm and eggs. • Explain the concepts of capacitation and the acrosome reaction in the context of fertilization.
Last update: Svobodová Zuzana, Mgr., Ph.D. (12.06.2025)
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