Midterm Cellular Biology PDF

CELLULAR BIOLOGY If you know everything in this document or if your aim is higher than the average, you should also read the Moodle slide. Good luck! CONTENT: BASICS OF CELL AND ORGANISM........................................................

CELLULAR BIOLOGY If you know everything in this document or if your aim is higher than the average, you should also read the Moodle slide. Good luck! CONTENT: BASICS OF CELL AND ORGANISM........................................................................................... 1 1. Definition of the cells............................................................................................................1 2. Fundamental basis unit of life:............................................................................................. 1 3. Domain of life:......................................................................................................................2 4. Prokaryotic and Eukaryotic cells..........................................................................................6 THE CHEMICAL COMPONENTS OF THE CELLS......................................................................7 1. Chemical bonds................................................................................................................... 7 2. Molecules in cells.................................................................................................................8 CELL STRUCTURE (Eukaryotic cell)....................................................................................... 14 1. Cell wall............................................................................................................................. 14 2. Cell membrane.................................................................................................................. 14 3. Protoplasm/ Cytoplasm/ Cytosol........................................................................................15 4. Endoplasmic reticulum (ER).............................................................................................. 16 5. Golgi.................................................................................................................................. 16 6. Ribosomes.........................................................................................................................18 7. Cytoskeleton (This part has a part of lecture 6).................................................................18 8. Lysosome...........................................................................................................................21 9. Peroxisome........................................................................................................................21 10. Mitochondria.................................................................................................................... 22 11. Chloroplasts..................................................................................................................... 22 12. Vacuoles.......................................................................................................................... 23 13. Cilia and Flagella............................................................................................................. 23 14. The nucleus (This part has a part of lecture 5)................................................................ 24 15. Distinguish features......................................................................................................... 27 PRINCIPLES OF TRANSMEMBRANE TRANSPORT............................................................... 28 1. Passive transport:.............................................................................................................. 29 2. Active transport:.................................................................................................................30  BASICS OF CELL AND ORGANISM 1. Definition of the cells - Cells are the basic structures of living organisms. - Cells are the basic building blocks of all living things. - The cell is the basic structural and functional unit of life forms. - Cells are the smallest common denominator of life. 2. Fundamental basis unit of life: Note: Để tránh bị nhầm lẫn giữa organ và tissue các bạn có thể đặt câu hỏi liệu cái đó có thực hiện bao nhiêu chức năng. Nếu bạn có thể liệt kê nhiều hơn 1 thì khả năng cao đó là organ. ○ Red blood cell (cell) ○ Xylem (tissue) ○ Liver (organ) ○ Leaves (organ) - We distinguish cells by size, shape, structure, and function. - Compare “Scheiden and Schwann proposed cell theory” to “Modern Cell Theory” Scheiden and Schwann proposed cell theory Modern cell theory - All living things are made of cells - The structural and functional unit of - Unit of structure, physiology, and organization all living things in living things. - Come from the pre-existing cell by - Retains a dual existence as a distinct entity division (spontaneous generation and a building block does not occur) - Free cell formation, similar crystals - Contains hereditary information - the (spontaneous generation - Thuyết tự sinh) same in chemical composition - All life’s energy flow (metabolism and biochemistry) occurs within cells. 1  - What is the most significant difference between the modern cell theory and the cell theory of Schleiden and Schwann? Scheiden and Schwann proposed cell theory Modern cell theory Free-cell formation is similar to the formation of All cells come from pre-existing cells crystals (spontaneous generation) by division 3. Domain of life: - There are 2 types of cells: Prokaryotic and Eukaryotic 2 a) Bacteria: - Unicellular, a few species have colonial lives for at least some of their lifetime (e.g. Cyanobacteria). - Lack of membrane-bound organelles and multicellular forms. - Include + Cyanobacteria (autotrophic – tự dưỡng): sun + water → single sugar + Other bacteria (heterotrophic – dị dưỡng): take the food → sugar - Small individually but they make up a significant part of the earth’s biomass - Structure of E. coli bacteria: + The nucleoid region contains genetic material. + Consists of an outer membrane, a periplasmic space, a cell wall, and an inner membrane. - Adapted for growth under many diverse conditions: + Mesophiles (warm), grow best at 25°C - 40°C + Psychrophiles (cold), grow best at 15°C - 20°C, some 0°C. + Thermophiles (hot), grow best at 50°C - 60°C, some can tolerate temperatures of 110°C b) Archare - Lack nuclei - Similar in size and shape(s) - Higher level compared to bacteria. - rRNA gene: Archaea were more closely related to eukaryotes than bacteria. - Include the most diverse extremophiles (SV ưa cực): + Acidophiles (acid): acidic (low) pH. + Alkaliphiles (base): high pH. + Toxicolerants (toxic): damaging elements (e.g., pools of benzene, nuclear waste). + Psychrophiles (cold): grow best at 15 °C or lower 3  + Thermophiles/ hyperthermophiles (hot): grow best at 40 °C or higher, or 80°C or higher. Pyrolobus fumarii (113°C) c) Protista: - Best defined as eukaryotes that are NOT fungi, animals, or plants. - They are polyphyletic (đa ngành) - A single cell or a colony of similar cells - Live in water, moist terrestrial habitats (môi trường ẩm ướt) - Parasites (ký sinh) and symbionts (cộng sinh) - Autotrophs (tự dưỡng), heterotrophs (dị dưỡng), or both - Reproduce asexually, some sexually d) Fungi - Decomposers – the best recyclers around - No chlorophyll – non-photosynthetic - Most multicellular (hyphae) – some unicellular (yeast) - Non-motile - Cell walls made of chitin - Are more related to animals than the plant kingdom e) Plantae - Multicellular, eukaryotes consist of a rigid structure that surrounds the cell membrane called the cell wall: cellulose - Non-motile - Reproduce sexually - Follows the autotrophic mode of nutrition - Contains photosynthetic pigments called chlorophyll in the plastids 4  - Classification of Kingdom Plantae: Bryophytes Thalophyta Pteridophytes Gymnosperms Angiosperms (small) Lack of a well- differentiated Well - body structure Differentiated differentiated Plant → Primitive Well - Well - plant body - Structures - body and simple differentiated differentiated Stem, leaf Stem, roof, body leaves. → Majority of aquatic Spore-dispersing Vascular x x ✓ ✓ vascular plant Naked and Seed Covered and x x x sprema: seed formation sprema: seed “exposed seed” Picture f) Animalia - Multicellular, heterotrophic eukaryotes that are capable of mobility for at least part of their life, and that have cells lacking cell walls. 5 4. Prokaryotic and Eukaryotic cells NOTES: - Multicellular and unicellular → 2 kiểu sinh vật - Single cell and multiple cells → 2 kiểu sinh vật - Prokaryotic and Eukaryotic → 2 kiểu tế bào 6  THE CHEMICAL COMPONENTS OF THE CELLS 1. Chemical bonds - C, H, O, N make up 96.5% of all the atoms in an organism - Electrolytes: K, Na, Cl, Mg, P, Ca, Fe, I - Covalent bonds (liên kết cộng hóa trị): + Electrons may be shared equally or unequally in covalent Bond + Electronegativity: affinities for electrons + Non-polar: the bonding electrons are shared equally between the two atoms Eg: in the case of most C-C; C-H bonds + Polar: bonded atoms have different electronegativities and unequal sharing of the electrons - Ionic interactions (liên kết ion): + Ionic bonds form by the gain and loss of electrons + In sodium chloride (NaCl), for example, the bonding electron contributed by the sodium atom is completely transferred to the chlorine atom - Hydrogen bonds (liên kết hydro): A hydrogen bond can form between two water molecules. - Van der Waals interactions: When any two atoms approach each other closely they create a weak, non-specific attractive force - Hydrophobic interactions (liên kết kị nước): In an aqueous environment, nonpolar molecules or nonpolar portions of larger molecules are driven together by the hydrophobic effect, thereby reducing the extent of their direct contact with water molecule 7 2. Molecules in cells - Water: + The most abundant substance in the cell accounts for about 70% of a cell’s weight + Most intracellular reactions occur in an aqueous environment + Water’s role as a solvent helps cells transport and use substances like oxygen or nutrients. + Carry molecules to the necessary location + Heat regulators 8 - Carbohydrates: + Sugars, and the larger molecules made from carbohydrates + The name of the covalent bond between 2 monomers in starch molecules is glycosidic. + Homogeneous polymers: contain only one kind of sugar/ considered to be ‘noninformational” + Heterogeneous polymers: contain 8-10 types of sugars + Glycogen – in humans and animals + Starch and cellulose – in plants + Functions Energy sources: glucose, glycogen, starch Structure support: cellulose, chitin Molecular markers: glycoproteins and glycolipid of cell membrane - Lipids + Non-polar; not soluble in water; soluble in non-polar solvents such as chloroform + Two different structural parts: Hydrophilic head (đầu ưa nước): chemical active Hydrophobic tail (đuôi kị nước): differences between hydrocarbon chains- not very active chemical + Functions: energy source Stored in the cytoplasm of many cells in the form of droplets of triacylglycerol molecules Produce about six times as much usable energy as glucose Animal fats (meat, butter and cream) Plant oils (corn and olive oil) 9 - Protein: + All have carboxylic acid group (COOH) and amino group (NH2) both linked to a single C-atom (α-carbon) + Differing Only in Their Side Chains Compose Proteins + Special amino acids: Cysteine Proline Glycine + Hierarchical Structure of Protein: Primary structure: the linear sequence of amino acids linked together by peptide bonds Secondary structure: folding of the polypeptide chain into local α helices or β sheets Tertiary structure: 2nd structure with various loops and turns 10  in a single polypeptide chain pack into a larger independently stable structure Quaternary structure: some individual polypeptides with their tertiary structures can associate into a quaternary structure – multichain complex + When a protein loses its higher-order structure, but not its primary sequence, it is said to be denatured. Factors: temperature, pH… + Denatured proteins are usually non-functional. + Functions: Regulation Structure Signaling Transport Catalysis Motor proteins 11 - Enzyme: + Help speed up metabolism, or the chemical reactions in our bodies, and do not chemically change at the end of the reaction + A small amount is needed to catalyze a lot of substrates. + Specific – each class of enzymes will catalyze only one particular reaction. + Enzymes catalyze reversible reactions + Many enzymes are only able to work within the presence of a coenzyme (or cofactor). + Affected by changes in temperature and pH + The substrate molecule fits into the active site of the enzymes like a key into a lock, forming an enzyme-substrate complex, a temporary structure. + Factors that affect the activity of enzymes: pH Temperature Concentration of enzyme Concentration of substrate - Nucleotides: The most important role → storage of biological information + RNA - ribonucleotides: A, G, C, U; mostly single-stranded + DNA - Deoxyribonucleotides (C5H10O4): A, G, C, T; double-stranded helix + One or more phosphate groups (H3PO4 ) + Bases Pyrimidines: all derive from six-membered pyrimidine ring ❖ Cytosine (C) ❖ Thymine (T) ❖ Uracil (U) Purines: have a second, five-membered ring fused to the six-membered ring ❖ Adenine (A) ❖ Guanine (G) 12 - Adenosine triphosphate (ATP) is a crucially important energy carrier in cells 13  CELL STRUCTURE (Eukaryotic cell) 1. Cell wall - Found in plants, fungi and bacteria - Found outside of the cell membrane - Non living layer - Function: Protection, structure, and support - Components: + Plants - cellulose + Fungi - chitin + Bacteria - peptidoglycan + Archaea - glycoprotein, S-layers, pseudo peptidoglycan, or polysaccharides 2. Cell membrane 14  - Living layer - Surrounds outside of all cells - Structure: + Double layer of phospholipids: impermeable barrier and stability Heads are hydrophilic (ưa nước) Tails are hydrophobic (kỵ nước) Three classes of membrane lipids: phosphoglycerides (derivatives of glycerol-3-phosphate, contains two esterified fatty acid chains), sphingolipids (derivatives of sphingosine- an amino alcohol with a long hydrocarbon chain), Sterols (contains a four-ring hydrocarbon) + Protein: transportation and cell recognition Integral proteins (Protein xuyên màng): mostly in α helix Peripheral proteins (Protein ngoại vi-protein bám màng): noncovalent interactions with integral proteins or membrane lipids + Carbohydrates: protect the cell, cell recognition, and adhesion - Functions: + Maintains homeostasis (Cân bằng nội môi) + Mediates cellular transport + Transmits cellular signals 3. Protoplasm/ Cytoplasm/ Cytosol - Protoplasm: cytoplasm and nucleus - Cytoplasm: all the content inside the cell membrane except the nucleus - Cytosol: the matrix of cytoplasm 15 4. Endoplasmic reticulum (ER) - Function: + Synthesis of cell products and transportation. + Connects to the nuclear envelope and cell membrane - Components: a network of hollow membrane tubules - Details: + Rough ER: Has protein on its surface Makes membrane proteins and export proteins. + Smooth ER: Makes membrane lipids Regulates calcium Destroys toxic substances 5. Golgi - Function: Receiving and shipping - Components: Stacks of flattened sacs - Mechanism: Receiving proteins from ER by cis face → completing the structure → packing proteins in new bags → fuse with the cell membrane for release from the cell from the trans face 16 17 6. Ribosomes - Function: “Protein factories” for cells: Creating proteins by protein synthesis. - Components: Protein and rRNA. + In prokaryotes and Mitochondria protein: 70S (50-S and 30S subunits). + In eukaryotes protein 80S (60S and 40S). Take advantage of this difference for medical uses + Mẹo nhớ: Proka: 357, Euka 468 - Details: + They are floating in the cytosol (make proteins that are required inside the cell) + Mostly located in rough ER (make protein for exporting or used inside). + Found also in Prokaryotes and Mitochondria. 7. Cytoskeleton (This part has a part of lecture 6) - Present in the cytoplasm of all cells, including bacteria, and archaea. - Function: + Maintain cell shape and intracellular transportation. + Movement + Organization and structural support that define the shapes of all cell 18 - Components: Proteins + Microfilaments (vi sợi): are threadlike and made of actin The structure: Actin monomers self-associate and polymerize into filaments ∼ 8 nm in diameter Functions: ❖ Maintain cell shape ❖ Muscle contraction ❖ Cytoplasmic streaming ❖ Cell motility ❖ Cell division (cytokinesis) + Microtubules (vi ống): are tube-like & made of tubulin: The structure of a small segment of a microtubule ❖ Each α tubulin and β tubulin binds a molecule of GTP (guanosine triphosphate) ❖ They continue to attach together into protofilaments. ❖ 13 protofilaments form a tube called heterodimers, with a diameter of about 25 nm. 19  Functions: ❖ Mitotic spindle (thoi phân bào) ❖ Form the core of motile structures: cilia and flagella ❖ Microtubules and motor proteins are even used by viruses, such as HIV and adenovirus, allowing the viruses to rapidly reach the nucleus and replicate → treatment ❖ Taxol (paclitaxel) binds to microtubules and makes them more stable by preventing tubulin subunits from dissociating → prevent mitosis → Used to treat ovarian and breast cancers ❖ Colchicine: causing a cell’s microtubules to disappear → Used to treat gout ❖ Zoxamide - a fungicide, binds specifically to fungal tubulins and prevents fungal growth Activity: Cells have two families of molecular motors that move on microtubules: ❖ Kinesins, which usually move toward the plus ends of microtubules ❖ Dyneins, which move toward microtubules’ minus ends 20  + Intermediate filaments (sợi trung gian): Structure: are major components of the cytoplasmic and nuclear cytoskeletons, made of various types of protein 8–12 nm thick and form resilient networks in the cytoplasm and nucleus. Functions: ❖ Structural support, resist mechanical stress ❖ Most intermediate filament genes in humans encode keratins, expressed in all different kinds of epithelial tissues of the body ❖ Defective intermediate filaments are the cause of many human diseases, eg: EBS (mutations in keratins K5 or K14 cause epithelial cell fragility, an inherited skin-blistering disorder) 8. Lysosome - Function: + Break down food, bacteria, and worn-out cell parts for cells + Program for cell death (apoptosis) + Release and lyse (activate) enzymes to break down + Recycle cell parts - Components: Digestive enzymes 9. Peroxisome - Function: Absorb nutrients, digest fatty acids, alcohol, cholesterol synthesis, and the digestion of amino acids - Components: + Small vesicles found around the cell + A single membrane contains oxidative enzymes - enzymes that require oxygen 21 10. Mitochondria - Have been conserved across evolution - Retains similarity to its prokaryotic ancestor - Function: energy factories that generate ATP, cellular respiration - Components: + A double membrane with an outer membrane and folds membrane is an inner membrane + The folds of the inner membrane are called cristae + The fluid contained in the mitochondria is called the matrix + The special feature is it contains its own ribosome (the 70S) and DNA 11. Chloroplasts - Function: Convert light energy of the Sun into sugars - can be used by cells (photosynthesis) - Components: + Double membrane: + Outer is smooth + Inner modified sacs - thylakoids: the grana particles are stacked on top of each other + Stroma-gel-like surrounding the thylakoid 22 12. Vacuoles - Function: Storage - Components: Fluid-filled sacks. - Small or absent in animal cells - Plant cells have a large Central Vacuole 13. Cilia and Flagella - Function: locomotion - Structure: + Cilia (lông): are shorter and more numerous in cells (Euka) + Flagella (roi): are longer but fewer on cells (Proka and Euka) 23 14. The nucleus (This part has a part of lecture 5) NOTES: + Nucleoli: nhân con (số nhiều) + Nucleolus: nhân con (số ít) + Nucleoid: vùng nhân không vỏ + Nucleus: nhân chuẩn (số ít) + Nuclei: nhân chuẩn (số nhiều) - The largest organelle - The nucleus may have arisen by endosymbiosis, a process in which one prokaryotic cell engulfs another cell, which then becomes a primitive nucleus - Function: contains hereditary material. - Components: + The nuclear envelope Double membranes The lumen is between two membranes and the lumen of the nuclear envelope is continuous with the lumen of the ER. 24  Contains numerous NPCs (phức hệ lỗ màng nhân - nuclear pore complex) ❖ Many different classes of molecules and macromolecules are transported through NPCs ❖ Uncharged molecules