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by: Udbluehen03

Lecture_1_pdf.pdf BISC401

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These are the notes we covered during the first week of class; chapter 1 (introduction) and chapter 2 (chemistry of life). I hope you find them very useful!
Molecular Biology of the Cell
Class Notes
Biology, molecularbiology, Chemistry




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This 11 page Class Notes was uploaded by Udbluehen03 on Saturday September 3, 2016. The Class Notes belongs to BISC401 at University of Delaware taught by Lachke,Salil in Fall 2016. Since its upload, it has received 131 views. For similar materials see Molecular Biology of the Cell in Biology at University of Delaware.


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Date Created: 09/03/16
Class 1 – 8/30/2016, Introduction to life, cells and genes Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish Living Organisms - All living things descended from a common ancestral cell - Water, inorganic ions and a wide array of relatively small molecules make up for 75% to 80% of living matter by weight - Every cell makes its molecules - Both large and small molecules are important to the cell. - Adenosine triphosphate (ATP) is the most common molecule used by cells to capture, store and transfer energy. o Currency of the cell Proteins - Most abundant and functionally versatile of the cellular macromolecule - 20 different amino acids in linear chains - Amino acids are obtained by either synthesizing them from other molecules or by breaking down proteins that we eat - Many proteins are enzymes (accelerate or catalyze chemical reactions) - Cytoskeletal protein o Provides structure  All life is classified into three groups o Bacteria o Archaea o Eukaryota  There are two distinctive types of cell o Prokaryotic cell o Eukaryotic cell Prokaryotic cell structure - Nucleoid, cytoplasm, inner membrane, cell wall, periplasmic space, and outer membrane - Closed compartment - Lack a defined nucleus - Simple internal organization - Two kingdoms o Eubacteria Class 1 – 8/30/2016, Introduction to life, cells and genes Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish o Archaea - Eubacteria or bacteria o Single celled organisms o Cyanobacteria o 1 – 2 µm - Some bacteria have an invagination of a cell membrane called a mesosome o Associated with synthesis of DNA and secretion of proteins - Bacteria mRNAs undergo limited if any processing - Escherichia coli (E. coli) o Most common experimental organism Eukaryotic cell structure - Extensive internal membrane that encloses the organelles - Enclosed nucleus - 10 – 100 µm in size - Cytoskeleton o Gives cell strength and rigidity o Maintains cell shape o Controls movement of structures within the cell o 3 classes of fibers compose the cytoskeleton o Microtubules  20nm in diameter  Built of polymers of the protein tubulin o Intermediate filaments  10nm in diameter o Microfilaments  7nm in diameter  Built of protein actin o The cytoskeletal fibers allow the formation of axons and dendrites - Nucleus o Largest organelle in animal cells o Outer nucleus membrane is continuous with the endoplasmic reticulum o Site of DNA replication and the synthesis of ribosomal RNA, mRNA and a large variety of noncoding RNA Nucleolus o Inside the nucleus Class 1 – 8/30/2016, Introduction to life, cells and genes Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish o Where ribosomal RNA is synthesized and ribosomes are assembled DNA o Deoxyribonucleic acid o Consists of two helical strands that are coiled, which forms a double helix. o Important in heredity o Composed of monomers called nucleotides o There are four different nucleotides  A, T, C, G o Sequence  Where genetic information carried by DNA is stored o The total DNA in an organism is called genome o Genes have two parts  The coding region  Specifies the amino acid sequence of a protein  The regulatory region  Binds specific proteins and control when and in which cell the gene’s protein is made o Most bacteria have a few 1000 protein-coding genes o Other unicellular eukaryotes have about 5000 o Humans and other metazoans have between 13,000 and 23,000 o Cells use 2 processes in series to convert the coded information in DNA into proteins  Transcription  Translation o Transcription  The protein-coding region of a gene is copied into a single-stranded ribonucleic acid(RNA) whose sequence is the same as one of the two in the double-stranded DNA  A large enzyme, RNA polymerase, catalyzes the linkage of nucleotide into an RNA chain using DNA as a template  The initial RNA product is processed into a smaller messenger RNA(mRNA) molecule  mRNA moves out the nucleus to the cytoplasm (region of the cell outside the nucleus) o Translation  Ribosome carries out translation Class 1 – 8/30/2016, Introduction to life, cells and genes Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish  Ribosome assembles and links together amino acid in the precise order dictated by the mRNA sequence according to the nearly universal genetic code. Endoplasmic Reticulum (ER) o Important in the synthesis of lipids, secreted proteins and many types of membrane proteins o Smooth ER  Lacks ribosome  Site of synthesis of fatty acids and phospholipids o Rough ER  Ribosomes present  Synthesis, processing and sorting of secreted proteins Golgi Complex o Processes and sorts secreted proteins and membrane proteins synthesized on the rough ER Lysosomes o Responsible for degrading many components that have become obsolete for the cell or organism o Contain a group of enzymes that degrade polymers into their monomeric subunits o All lysosomal enzymes are called acid hydrolases; they work best at acidic pH values. Peroxisomes o Contain several oxidases, enzymes that use molecular oxygen to oxidize organic substances and in the process form hydrogen peroxide o Contain copious amounts of the enzyme catalase, which degrades hydrogen peroxide to yield water and oxygen o Plants seeds contain glyoxisomes  Oxidize stored lipids as a source of carbon and energy for growth  Similar to peroxisomes Class 1 – 9/1/2016, Chemistry of Life Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish Similar genes control development of same organs in diverse animals. - For example, the Pax6 o Pax6 is a protein encoded by Pax6 gene o Important in eye and brain development, although, it does not fully control the development of the eye o The expression of Pax6 in fly, mouse and human results in normal eyes o The removal of Pax6 results in absence of eyes o Expression of Pax6 induces extra eyes Some of the tools used in molecular biology - Many sophisticated tools are used - 2D gel electrophoresis o Used in the separation of proteins - Gene array technology o Used in the study of nucleic acid like DNA Chemistry of life - There are four key concepts - Molecular complementarity o Basis of biomolecular interactions - Chemical Building blocks o Small molecules serve as building block for larger structures - Chemical equilibrium o Reversibility of chemical reactions ???????? o ???? ???????? = ???????? - Chemical bond energy o How life follows laws of thermodynamics o Hydrolysis of the molecule ATP is the source of energy for chemical reactions Weak and strong interactions - Weak + strong interactions = molecular glue - Weak interactions o Non covalent bonds Class 1 – 9/1/2016, Chemistry of Life Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish - Strong interactions o Covalent bonds Most fundamental elements in biological molecule Names Number of covalent bonds that can be formed Carbon 4 Oxygen 2 Phosphorus 5 Hydrogen 1 Nitrogen 3 or 4 Sulfur 2, 4, or 6 - they all readily form covalent bonds - each has a defined geometry that is determined by the atom’s a) size, b) electron distribution around the nucleus, c) number of electrons shared Importance of phosphorus - backbone of nucleic acid - used in the regulating protein activity - Important in signaling GTP - Helps in the phosphorylation of amino acid - ATP contains three phosphate groups - Amino acids o Serine o Threonine o Tyrosine Importance of functional groups - Functional groups give molecules specific chemical properties - Gives specific arrangements of atoms that confer distinctive chemical properties to the molecules that contain them. Class 1 – 9/1/2016, Chemistry of Life Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish  Single bonds can rotate freely while double or triple bonds can’t  A carbon atom bonded to 4 different atoms in a nonplanar configuration is called asymmetric  Different stereoisomers of a molecule have different functions o For example, one stereoisomer of ketamine is an anesthetic, whereas the other causes hallucinations. Electronegativity - The ability of an atom to attract electron - Similar electronegativity = non polar bond o Equal sharing of bonding electrons - Dissimilar electronegativity = polar bond o Unequal sharing of bonding electrons - O-H bond possess an electric dipole o The dipole moment in water permanent o Can form hydrogen bonds other molecules o The dipole moment allows water to form electrostatic, noncovalent interactions Covalent bonds - Two atoms share a single pair of electrons - When they share multiple pairs of electron, they form multiple bonds - Stable in room temperature and body temperature - Double bonds require more energy to break than single bonds - Thermal energy at room temperature is 0.6 kcal/mole, which is greatly lower than the energy for covalent bond (this is why it is stable at room temperature) o For example, C-C bond is 83 kcal/mole Noncovalent bonds - The energy required to break non covalent bond is 1-5 kcal/mole o This makes the covalent bonds stronger - Constantly being formed and broken in room temperature Class 1 – 9/1/2016, Chemistry of Life Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish - Multiple noncovalent interactions can act together to form a highly stable molecule - There are four types o Ionic interactions o Hydrogen bonds o Van de Waals forces o Hydrophobic effect - Ionic interactions o Attraction between positively charged ion (a cation) and a negatively charged ion (an anion)  For example, NaCl o No fixed or specific geometry orientations o The electrostatic field around an ion is uniform in all directions o Solubility in water depends on interactions with water molecules o When ions are in solution, they are surrounded by a hydration shell of water molecules o The strength of the interaction between two opposite charged ions depends on the concentration of the other ions in a solution - Hydrogen bonds o Interaction of a partially positively charged hydrogen atom in a dipole with unpaired electrons from another atom either in the same or in a different molecule. o Hydrogen bonds allow uncharged molecules to dissolve in water. - Van de Waals forces o Results due to formation of transient dipole when two atoms are close  Transient dipole – when electrons of one atom perturb electrons of the other o The strength of van de Waals interaction decreases rapidly with increasing distance o When atoms get too close together they repel one another - Hydrophobic effect o When nonpolar molecules or nonpolar part of molecules tend to aggregate in water o Water molecules can’t form hydrogen bonds with nonpolar substances so they form “cages” of relatively rigid hydrogen bonded pentagons and hexagons around nonpolar molecules  Energetically unfavorable because it decreases entropy or randomness of the population of water molecules. Class 1 – 9/1/2016, Chemistry of Life Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish o Aggregation of nonpolar molecules reduces the number of water molecules involved in forming highly ordered cages, which increases entropy – making it more energetically favorable.  Macromolecules are held together by a combination of weak bonds. - For example, the Ab-Ag interaction Kinetic energy - Energy of movement - For example, the motion of molecules Potential energy - Stored energy - For example, energy stored in covalent bonds Thermal energy - A form of kinetic energy - Heat - For heat to do work, it must flow from a region of higher temperature to a region of lower temperature Radiant energy - A form of kinetic energy - Kinetic energy of photons or waves of light - Can be converted to thermal energy - Can change the electronic structure of the molecules by moving electrons into higher energy orbitals Mechanical energy - A form of kinetic energy - Results from the conversion of stored chemical energy Electric energy - A form of kinetic energy - The energy of moving electrons or other changed particles Chemical potential energy - A form of potential energy Class 1 – 9/1/2016, Chemistry of Life Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish - The energy stored in the bonds connecting atoms in molecules Concentration gradient potential energy - A form of potential energy - Generates ATP Electric potential - A form of potential energy - Energy of charge separation Chemical Reactions - There are two types o Endergonic and exergonic Exergonic - Product contains less energy that reactants Endergonic - Product has more energy than reactant - Energy is absorbed during the reaction Gibb’s law - System change to minimize free energy - ΔG = G product – G reactant - If ΔG is negative, the forward reaction is spontaneous (it does not mean it will occur spontaneously) o Energy will be released as the reaction takes place o Exergonic reaction o Thermodynamically favorable - If ΔG is positive, the forward reaction is not spontaneous o Energy is needed to force the reactants to become products o Endergonic reaction - If ΔG is zero, both forward and reverse reactions will occur at equal rates o The system is at equilibrium Activation energy - Energy needed to excite reactants to a higher energy stable Class 1 – 9/1/2016, Chemistry of Life Dr. Salil Lachke th Molecular Cell Biology, 8 edition - Lodish - Catalysts, like enzymes, lower the activation energy required to start the reaction


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