MED1003 Molecules, Cells and Genes Lecture (PDF)

MED1003 Molecules, Cells and Genes by Siu Wai (Phyllis) TSANG, PhD TUNG WAH COLLEGE email: [email protected] Office#: 3190-6713 Prepared by SWT 2024 email: [email protected] 1 Week Date...

MED1003 Molecules, Cells and Genes by Siu Wai (Phyllis) TSANG, PhD TUNG WAH COLLEGE email: [email protected] Office#: 3190-6713 Prepared by SWT 2024 email: [email protected] 1 Week Dates of Topics Meetings (Lecture / Seminar) Remarks 1 L: Sept. 3, 2024 S: Sept. 5 or 6 Course introduction A preview of the Cell MED1003 2 L: Sept. 10, 2024 S: Sept. 12 or 13 L: Sept. 17, 2024 The macromolecules of the cell Online materials (Mid-autumn festival) No class Molecules, Cells and Genes 3 S: Sept. 19 or 20 Cells and organelles Membranes: structure, function, chemistry L: Sept. 24, 2024 4 and transport S: Sept. 26 or 27 Discovery of cells and microscopy 5 L: Oct. 1, 2024 Online materials (National Day) No class Lecture: Tuesday 17:00 – 18:50 S: Oct. 3 or 4 The endomembrane system and peroxisomes Cytoskeletal systems and extracellular L: Oct. 8, 2024 6 structures S: Revision session Online submission of assignment Assignment 1 Seminar session 1: Fri 11:00 – 11:50 7 L: Oct. 15, 2024 Mid-term test Seminar session 2: Fri 09:00 – 09:50 S: Oct. 17 or 18 Cellular respiration 8 L: Oct. 22, 2024 Signal transduction mechanism I Seminar session 3: Thur 17:00 – 17:50 S: Oct. 24 or 25 L: Oct. 29, 2024 Seminar session 4: Thur 13:00 – 13:50 9 Signal transduction mechanism II S: Oct. 31 or Nov 1 L: Nov. 5, 2024 10 The cell cycle, DNA replication and mitosis S: Nov. 7 or 8 L: Nov. 12, 2024 Sexual reproduction, mitosis, meiosis and 11 S: Nov. 14 or 15 genetic recombination Project due L: Nov. 19, 2024 Genes and chromosomes 12 S: Nov. 21 or 22 The regulation of gene expression L: Nov. 26, 2024 Cancer cells 13 S: Nov. 28 or 29 In class assignment Assignment 2 L: Dec. 3, 2024 Current research of cellular study 14 S: Dec. 5 or 6 Revision Prepared by SWT 2024 email: [email protected] 2 Course assessment 1. Written assignments (10%) Assignment 1: Week 6, online submission by Oct. 12, 2024 Assignment 2: Week 13, in-class assignment on Nov. 28 or 29, 2024 2. Mid-term test (20%) Week 7, Oct. 15, 2024 3. Project (30%) Due on week 11, Nov. 14 or 15, 2024 4. Examination (40%) Mid December 2024 Prepared by SWT 2024 email: [email protected] 3 Textbook of MED1003 Becker’s World of the Cell 10th ed. Publisher: Benjamin-Cummings / Pearson ISBN13: 9780137441778 (10th) ISBN13: 9780321934925 (9th) Prepared by SWT 2024 email: [email protected] 4 A preview of the Cell Prepared by SWT 2024 email: [email protected] 5  The basic vital units Cells are the basic vital units that exhibit the fundamental activities common to all forms of life 細胞是基本的生命單位 Every organism either consists of cells or itself a single cell Multicellular 多細胞 or unicellular 單細胞 organisms Cells are of different shapes and sizes Cell 細胞 NOT a vital unit Prepared by SWT 2024 email: [email protected] 6  https://www.sciencealert.com/images/2018- 04/processed/microbe_body_ratio_new_cover_1024.jpg Textbook Ch.1 p.27 Prepared by SWT 2024 email: [email protected] 7 The basic vital units (cont’d) From organism to organism, the count of cells may vary Humans are made up of trillions of cells A bacterium is made up of only one cell Cells have the capability to grow, reproduce and become specialized Once specialized, the cells have the ability to respond to stimuli and adapt to changes in the environment Herr Carl Nägeli (1844) is the person who first observed cell division during the formation of pollens All cells arise from pre-existing cells Prepared by SWT 2024 email: [email protected] 8 Functions of the cells provide structure and support facilitate growth through mitosis allow passive and active transport produce energy create metabolic reactions aid in reproduction Prepared by SWT 2024 email: [email protected] 9  Prepared by SWT 2024 email: [email protected] 10 Can we observe cells? Textbook Ch.1 p.30 Cellular dimensions Cells and cellular structures are very small Micrometer (µm, called micron 微米) is the most useful unit for expressing the size of cells A micrometer is one-millionth of a meter (10-6 m) Textbook Ch.1 p.30 1 cm = 10 mm 1 mm = 1,000 µm 1 cm = 10,000 µm Bacterial cells: a few µm in diameter Animal cells and plant cells: ~ 10−20 times larger Prepared by SWT 2024 email: [email protected] 11 Observation of cells in the old days Started by European scientists focusing on microscopes In 1665, Robert Hooke built a microscope (30×) to examine a thin slice of cork, he called the small boxes the “cells” These small boxes were dead plant cells “Cells” mean little rooms in Latin cork http://player.slideplayer.com/24/ 6961464/data/images/img3.jpg Prepared by SWT 2024 email: [email protected] 12 The use of microscopes Most cells are only visible with the use of a microscope Very few types of cells can be seen without using a microscope Prepared by SWT 2024 email: [email protected] 13 The chemistry of the Cell Prepared by SWT@TWC 2022-23 S1 14 Understanding the chemistry of the cell Five principles important to cell biology 1. The importance of carbon 2. The importance of water 3. The importance of selectively permeable membranes 4. The importance of synthesis by polymerization of small molecules 5. The importance of self-assembly Prepared by SWT 2024 email: [email protected] 15 1. The importance of carbon The carbon atom (C) is considered the most important atom in biological molecules Almost without exception, compounds of importance to the cell biologist have a backbone, or skeleton, of carbon atoms linked together covalently in chains or rings The study of carbon-containing compounds is the domain of organic chemistry Life on earth would NOT be possible without carbon; there are ~10 million carbon-based compounds Prepared by SWT 2024 email: [email protected] 16 Where can we find carbon atoms? Prepared by SWT 2024 email: [email protected] 17 Carbon: valence of four Specific bonding properties of carbon account for the characteristics of carbon-containing compounds An extremely important property of the C atom = Valence of four Carbon forms FOUR chemical bonds with other atoms Atoms can bond to each other via their outer electrons, and atoms are usually the most stable when they are surrounded by a total of EIGHT electrons, satisfying what is known as the octet rule The outermost electron orbital of a carbon atom has 4 electrons Carbon lacks 4 of the 8 electrons needed to make it the most stable Textbook Ch.1 p.46 Prepared by SWT 2024 email: [email protected] 18 Carbon: covalent bond Carbon atoms associate with each other or with other electron-deficient atoms, allowing adjacent atoms to share a pair of electrons Atoms that share electrons in this way are Textbook Ch.1 p.46 held together = joined by a covalent bond The sharing of one pair of electrons between atoms results in a single bond Two or three pairs of electrons can be shared by two atoms, giving rise to double bonds or triple bonds Prepared by SWT 2024 email: [email protected] 19 Stability of organic molecules The stability of organic molecules is expressed as bond energy The amount of energy required to break 1 mole (~6 × 1023 molecules) of such bonds Bond energies are usually expressed in calories per mole (cal/mol) A calorie (cal) is the amount of energy needed to raise the temperature of 1 gram of water by 1°C A kilocalorie (kcal) is equal to 1000 calories It takes a large amount of energy to break a covalent bond e.g., the carbon-carbon (C−C) bond has a bond energy of 83 kilocalories per mole (kcal/mol) Prepared by SWT 2024 email: [email protected] 20 Bond energy The bond energies for carbon-nitrogen (C−N), carbon-oxygen (C−O) and carbon-hydrogen (C−H) bonds are 70, 84, and 99 kcal/mol respectively in the same range of C−C bond (i.e., 83 kcal/mol) To break a carbon-carbon double bond (C=C), it Textbook Ch.1 p.47 needs 146 kcal/mol, or a carbon-carbon triple bond (CC), it needs 212 kcal/mol More covalent bonds make the chemical structure more stable Prepared by SWT 2024 email: [email protected] 21 Carbon-containing molecules Carbon-containing molecules are diverse due to the tetravalent nature of the carbon atom Long chains of carbon atoms can be built up; ring compounds are also common When only hydrogen atoms are bonded to carbon atoms in linear or branched chains or in rings, the resulting compounds are called hydrocarbons In biology, hydrocarbons play only a limited role because they are essentially insoluble in water Textbook Ch.1 p.48 Prepared by SWT 2024 email: [email protected] 22 Functional groups Specific arrangements of atoms that confer characteristic chemical properties on the molecules to which they are attached Carboxyl and phosphate groups (negatively charged) Amino groups (positively charged) Hydroxyl, sulfhydryl, carbonyl and aldehyde groups (uncharged; but polar 極性) Textbook Ch.1 p.48 Prepared by SWT 2024 email: [email protected] 23 Bond polarity In polar bonds, electrons are not shared equally between two atoms Bonding electrons attracted more strongly by one atom than by the other 4d45-912d-b662d1e09ba0/OCR_PolarCovalentBonds.en.x512.png https://labster-image-manager.s3.amazonaws.com/236cf7dd-0b06- content/uploads/2023/03/water-1024x614-1.png https://chemistrytalk.org/wp- Polar covalent bonds in H2O Polar covalent bonds in HCl Prepared by SWT 2024 email: [email protected] 24 2. The importance of water Water has an indispensable role as the universal solvent in biological systems Water is the single most abundant component of cells and organisms Typically, ~75–85% of a cell by weight is water Many cells depend on an extracellular environment that is essentially aqueous (e.g., cell is bathed) The most critical attribute of water is its polarity Water molecules are polar Prepared by SWT 2024 email: [email protected] 25 Characteristics of water molecules Unequal distribution of electrons gives water its polarity bent The water molecule is bent rather than linear in shape The two H atoms bonded to the oxygen at an angle of 104.5° Textbook Ch.1 p.52 Although the water molecule as a whole is uncharged, its electrons are unevenly distributed The oxygen atom is highly electronegative— it tends to draw electrons toward it the O atom has a partial negative charge δ - Prepared by SWT 2024 email: [email protected] 26 Hydrogen bond Water molecules are attracted to each other => hydrogen bonds Textbook Ch.1 p.52 electronegative O atom · electropositive H atoms a type of electrostatic attraction one-tenth as strong as a covalent bond Water is characterized by an extensive 3-D network of hydrogen-bonded molecules The hydrogen bonds between adjacent molecules are constantly being broken and re-formed half-life = a few microseconds Prepared by SWT 2024 email: [email protected] 27 Cohesion of water Each water molecule in the liquid state is hydrogen-bonded to at least three, usually four, neighbor molecules at any given time The tendency to form hydrogen bonds between adjacent molecules that makes water so highly cohesive Cohesiveness accounts for the high surface tension of water, and its serving as an Hydrogen e57nK1KJcVN_hydrogen_bonding.jpg https://useruploads.socratic.org/inbsj0OT9 excellent solvent bond Prepared by SWT 2024 email: [email protected] 28 Adhesion of water Adhesion of water is the force of water molecules stick to other substances public/styles/side_image/public/thumbnails/image/Adhesion_cohesion.png?itok=BaVqO8Au https://d9-wret.s3.us-west-2.amazonaws.com/assets/palladium/production/s3fs- https://labster-image-manager.s3.amazonaws.com/v2/H2O/41625b76-e166-4621-bc0f-b47324a4d741/H2O_HoldingHands_V01.en.x512.png Prepared by SWT 2024 email: [email protected] 29 Adhesion of water (cont’d) Adhesion of water is important in allowing water to move upward through the conducting tissues of plants → high surface tension The high surface tension also allows some insects to move across the surface of a pond without breaking the surface Textbook Ch.1 p.52 Prepared by SWT 2024 email: [email protected] 30 Solvent A solvent is a fluid in which another substance, called the solute, can be dissolved Water is an especially GOOD solvent for biological purposes because of its remarkable capacity to dissolve a great variety of solutes It is the polarity of water that makes it so useful as a solvent Textbook Ch.1 p.53 For NaCl to dissolve, solvent molecules must overcome the attraction of the Na+ cations and Cl- anions for each other Prepared by SWT 2024 email: [email protected] 31 Affinity for water Solutes that have an affinity for water and therefore dissolve readily in water are called hydrophilic (“water-loving”) Most small organic molecules found in cells are hydrophilic Polar molecules and ions are hydrophilic Molecules that are NOT soluble in water are termed hydrophobic (“water-fearing”) Important hydrophobic compounds found in cells are the lipids and proteins found in biological membranes Nonpolar molecules are hydrophobic Some biological macromolecules, notably proteins, have both hydrophobic and hydrophilic regions, so some parts of the molecule have an affinity for water whereas other parts of the molecule do not Prepared by SWT 2024 email: [email protected] 32 3. The importance of selectively permeable membranes Every cell (or organelle) needs some sort of physical barrier to keep its contents in and external materials out A cell also needs some means of controlling exchange between its internal environment and the external environment, across the barrier Such barrier (i.e., membrane) should be Impermeable to much of the cell contents Semi-permeable, allowing some materials moving in and out of the cell Insoluble in water to maintain the integrity of the barrier Permeable to water to allow flow of water in and out of the cell Prepared by SWT 2024 email: [email protected] 33 The properties of cell membranes A cell membrane (a.k.a. plasma membrane) is a selectively permeable barrier that consists of phospholipids, glycolipids and membrane proteins Most membrane lipids and proteins have both hydrophilic and hydrophobic regions, i.e., they’re amphipathic molecules The polar heads of membrane face Textbook Ch.2 p.55 outward to the aqueous environment The hydrophobic tails are oriented inward Prepared by SWT 2024 email: [email protected] 34 Membrane component: phospholipid 磷脂 A phospholipid is formed when two fatty acid tails and one phosphate-linked head group are attached to glycerol The two fatty acid tails are hydrophobic (water-fearing), but the phosphate head group is hydrophilic (water-loving) images/352079e6dc783dce573875198fcb364180b01331.png https://cdn.kastatic.org/ka-perseus- 親水 Phospholipids are “amphipathic 兩親性” molecules with one end of the molecule is 疏水 hydrophobic and the other end is hydrophilic. Copyright © Campbell’s Biology, Pearson Education, Inc. Prepared by SWT 2024 email: [email protected] 35 Phospholipid bilayer The bilayer keeps the internal environment of the cell at homeostasis despite changes in the environment The bilayer allows certain materials moving into or out of the cell is called selective permeability https://slideplayer.com/8950611/27/images/slide_1.jpg Prepared by SWT 2024 email: [email protected] 36  Selectively permeable to solutes Molecules that are hydrophobic can easily pass through the cell membrane, if they are small enough, because they are water-hating like the interior of the membrane Molecules that are large / hydrophilic cannot pass through the cell membrane without help The selective permeability of the bilayer allows for cells to take in things they need, like nutrients, but to keep unwanted materials or pathogens out of the cell https://i.stack.imgur.com/agHjI.jpg 37 Prepared by SWT 2024 email: [email protected]  Membrane proteins TWO major categories: integral and peripheral https://cdn.kastatic.org/ka-perseus-images/234a6b91810a43e7e7ea3e9cbe8c60dee6ad3cee.png 1. Integral membrane proteins integrated into the membrane; anchor to the hydrophobic core of the phospholipid bilayer extend all the way across the membrane → transmembrane 2. Peripheral membrane proteins found on the outside surfaces of membranes (either the external side or internal side) NOT stick into the hydrophobic core of the membrane 38 Prepared by SWT 2024 email: [email protected] 4. The importance of synthesis by polymerization of small molecules Most cellular structures are made of ordered arrays of linear polymers called macromolecules Important macromolecules in the cell include proteins, nucleic acids (both DNA and RNA), polysaccharides and lipids Prepared by SWT 2024 email: [email protected] 39  Cellular hierarchy Most cellular structures are composed of small, water-soluble organic molecules Small organic molecules (called monomers) polymerize to form macromolecules Macromolecules may function on their own, or they can be assembled into a variety of supramolecular structures Supramolecular structures are components Textbook Ch.2 p.57 of organelles & other subcellular structures All together make up the cell itself 40 Prepared by SWT 2024 email: [email protected] 5. The importance of self-assembly Molecular self-assembly The spontaneous folding of macromolecules and the interactions of these macromolecules to form more complex structures is inherent in the polymers themselves e.g., the native (natural) conformation of a protein the coiling and folding necessary to form a functional 3-D protein from one or more linear chains of amino acids, i.e., polypeptides TWO types of self-assembly Strict self-assembly: no factors other than the polypeptide sequence itself are needed Assisted self-assembly: requires a specific molecular chaperone to ensure that the correct conformation predominates over incorrect forms Prepared by SWT 2024 email: [email protected] 41 Self-assembly of a protein Prepared by SWT 2024 email: [email protected] 42  All about carbon https://kahoot.it/solo/?quizId=66bdbc3d-1c1b-4bb6-97fe- Kahoot! Game 07b2d39ca172 Prepared by SWT 2024 email: [email protected] 43 ~ The end ~ Thank you ! Prepared by SWT 2024 email: [email protected] 44