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Bio 02- Study Guide. Chapters 1 & 2

by: Cecilia Hernandez

Bio 02- Study Guide. Chapters 1 & 2 Bio 002

Cecilia Hernandez

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This study guide covers Chapters 1 & 2 for Bio 02. For chapter 1 it covers the Cell, Cells under the microscope, Prokaryotic Cell, Eukaryotic Cells, Model Organisms. Chapter 2 focuses on chemical b...
Dr. Kamal Dulai
Study Guide
Biology, Chemistry, cells, Prokaryotic Cells, eukaryotic cells, hydrogen bonds, ionic bonds, covalent bonds, Macromolecules
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This 11 page Study Guide was uploaded by Cecilia Hernandez on Sunday September 11, 2016. The Study Guide belongs to Bio 002 at University of California - Merced taught by Dr. Kamal Dulai in Fall 2016. Since its upload, it has received 100 views. For similar materials see INTRODUCTION TO MOLECULAR BIOLOGY in Biological Sciences at University of California - Merced.

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Date Created: 09/11/16
STUDY GUIDE- BIO 02 CHAPTER 1 Cells:The fundamental units of life:  Cell biology = the study of cells along with their structure, function, and behavior (focuses on its characteristics) Cells vary in their appearance & function:  Cell chemical requirements: o Need oxygen to live (aerobic) but some cells are poisoned by oxygen (anaerobic) o Consume more than air, sunlight, and water as part of raw materials o Need a complex mixture of molecules which are produced by other cells  Difference in size, shape, and chemical requirements reflect on the cells ability to perform its functions. Living cells all have a similar basic chemistry:  DNA Polymers chains are made of the same set of 4 monomers referred as nucleotides  Central Dogma: DNA (the information encoded gets transcribed into...)RNA (gets transcribed into a..)Protein  Proteins are made from amino acids  There are about 20 amino acids Cells Evolve:  Cells reproduce by replicating its DNA and dividing into two  Mutations can change the offspring whether for worse, better, or neutral  Evolution is the process when living species are modified to adapt to the environment Genes:  Genome = the sequence of nucleotides within an organism DNA which tells the cell how to function or behave  Different cells are able to express different genes  Theory of Evolution = Natural Selection and Random Variation gave rise to organism that share a common ancestry Cell Theory:  All living organisms are composed of 1 or more cells  Cells are the smallest units of life  New cells come from pre-existing cells PANEL 1-1 Light Microscope:  Allowed examination of the cells and its components  Visible light was used to illuminate the specimens  Viewing a very thin slice of tissue, the tissue is divided into thousands of many small cells  The cells may be closely packed or separated from one another by an extracellular matrix  Each cell is about 5- 20μm (micrometers) in diameter Fluorescence Microscopy:  Dyes are used to stain the cells  Illuminating light passes through 2 sets of filters Electron Microscopy:  Used beams of electrons as a source of illumination  It allowed the visibility of the cell to be in fine details including larger molecules  Highest magnification with the best resolution  Sections have to be much thinner and no possible way of viewing living or wet cells. Fluorescent Probes:  The dye absorbs light at one wavelength and emits it at a longer wavelength  The dye binds to a certain molecule in cells which show their location when examining it Confocal Microscopy:  It builds up an image by scanning the specimen with a laser beam  The detector allows only the fluorescence emitted within a certain point to be included in the image  Scanning the beam creates a sharp image Transmission Electron Microscopy:  Looking at thin sections of tissue  Transmits a beam of electrons instead of a beam of light through the sample ST nd rd  Process: 1 needs to be chemically fixed, 2 it needs to be embedded in plastic, 3 it needs to be cut in very thin sections, and lastly, it needs to be stained with salts of uranium and lead. Scanning Electron Microscopy:  Scatters electrons off the surface to look at the surface detail of the cells and other structures  The specimen is coated with a thin film of heavy metal  Then it is scanned by a beam of electrons by magnetic coils acting as lenses  The amount of electrons is measured by the detector  To resolve details in great focus it can be focused between 3-20 nm (nanometers) The Prokaryotic Cell:  Size: 0.5μm – 20μm  Most diverse and numerous cells on Earth  Lack a nucleus but still contain DNA  Divide by binary fission  No membrane enclosed organelles  Have a tough protective coat  Some are aerobic and others are anaerobic  Domain: o Bacteria: have the simplest structure  Live in the soil and some makes us ill  No organelles, not even a nucleus to hold its DNA o Archaea: Extremophiles- “lovers of extremes”  Live in extreme conditions such as high salt content, acidity, high methane level, and high temperaturs (Hyperthermophiles).  Cell Shape…:  For Bacteria: o Rods and helical shapes  For Archaea: o Spheres  Coccus o Rods  Coccobacillus o Comma- Shaped  Vibrio o Spiral shaped & flexibeSpirochete o Spiral shaped & rigdSpirillum The Eukaryotic Cell:  Size: 10μm - 500μm (Are bigger than prokaryotic cells)  Has a nucleus which contains DNA  Some live independent lives as a single celled organism & others live in multicellular forms  Domain: Eukarya  Kingdom: Plants, Animals, Protist, and Fungi  Divides through Meiosis or Mitosis  Contains enclosed organelles Organelles:  Nucleus: o Inside it has chromosomes and a network of proteins called the nuclear matrix o This organelle has a double membrane  Enclosed within 2 concentric membranes known as nuclear envelope  Nuclear envelope contains DNA  Mitochondria: o Found in eukaryotic cells o Makes ATP (Adenosine Triphosphate)  Produces ATP from the oxidation of food molecules like sugar o Takes in oxygen and releases carbon dioxide known as Cellular Respiration o Without Mitochondria, eukaryotic kingdoms (Plants, animals, & fungi) wouldn’t be able to use oxygen in order to release energy from food molecules o Contains a double membrane o Contains its own DNA o Thought to have evolved from bacteria  Chloroplasts: o Found in ONLY plant and algae o Contains the green pigment that makes the plant green o Carry out photosynthesis:  Trapping energy of sunlight and using that energy to continue the process in creating energy rich molecules…release oxygen o Get their energy from sunlight o Contains its own DNA o Thought to have evolved from (photosynthetic) bacteria as well  Internal Compartments: o Golgi Apparatus  Modification, sorting, and secretion of lipids & proteins  Modifies & packages molecules made in the ER which is either secreted or transported to another cell compartment o Lysosomes  Small & irregular shaped organelle  Releases nutrients from ingested food particlesbreaks down unwanted moleculesit gets recycle in the cell or excreted from the cell  Many molecules are broken down and remade o Peroxisomes  Hydrogen peroxide used to break down toxic molecules o Transport vesicles  An enclosed membrane organelle which transports materials from one place to another  Used in transporting materials starting from the ERGolgi Apparatuslysosomesand finally outside of the cell  It pinches off from a membrane and fuses to another organelle  Endocytosis: vesicles are formed by the process of pinching off and carry material gathered from the outside to be transported inside the cell  Exocytosis: vesicles inside the cell carry out the material outside o Rough ER (Rough Endoplasmic Reticulum)  Studded with ribosomes  Protein Sorting: Proteins are first directed to the ER then to their specific organelle  Insertion of membrane proteins: Membrane proteins are first inserted in the Rough ER as the protein is being synthesized  Glycosylation: The attachment of carbohydrates to proteins and lipids o Smooth ER (Smooth Endoplasmic Reticulum)  Lacks ribosomes  Functions: 1.) Metabolism – provides an increase Surface Area  2.) Storage of C???? : Contains calcium pump that transports calcium into the lumen  3.) Lipid synthesis & modification: Smooth ER is the primary site for the synthesis of phospholipids  Enzymes is necessary in the Smooth ER for certain modifications of the lipid cholesterol needed to produce estrogen and testosterone o Ribosome  Protein builders also known as the protein synthesizers of the cell  Connecting amino acids creating a long chain  Cytosol: o It’s part of the cytoplasm o Largest single compartment o Contains many large & small molecules which acts like a water based gel o Site of many chemical reactions… for example, the breakdown of molecules  Cytoskeleton: o Composed of actin filaments, microtubules, and intermediate filaments  Actin filament: thinnest filaments & responsible for muscle contraction  Microtubules: thickest filaments, hollow tubes, and helps pull the duplicate chromosomes in opposite directions  Intermediate filaments: serve to strengthen the cell o Combining the filaments and microtubules it helps give the cell such as mechanical strength, shape, and allowing it to move. o It’s outside the membrane bound organelle but inside the plasma membrane  Cytoplasm: o Throughout the cytoplasm, motor proteins are used to carry organelles & proteins  Plasma Membrane: o Controls the movement of the substance o Site of cell signaling Model Organisms:  E. coli: o Small and rod shaped cell o Lives in the human gut & other vertebrates o Grows rapidly o Purpose- knowing how the cells replicate their DNA and understanding how decoding these genetic instructions to make proteins  Brewer’s Yeast: o Also known as S. Cerevisiae o Small, single-celled fungus o Contains chloroplast but not mitochondria o Produces rapidly o Purpose for studying yeast- to gain a better understanding of the cell division cycle  Arabidopsis (Model Plant): o Learning about the three domains (Bacteria, Archaea, & Eukarya) o Studying a particular plant helps on learning about other plants o Purpose- gaining an insight of the development and physiology of the crop plants including the evolution of plant species  Fruit Fly (Drosophila melanogaster): o Purpose- providing proof that genes are in fact carried on chromosomes o Learning more about human development & disease  Nematode (Worm): o Attacks roots of crops o Inside the worm it has 70% of the human genes. C. elegans and Drosophila also contain human genes o Purpose- learning about apoptosis (it’s a programmed cell death) which is important for cancer research  Zebrafish: o It’s transparent for 2 weeks of its life o Purpose- observing how the cells behave during development  Study Human beings & their cells: o Human cells are kept in controlled environment o Exposed to hormones & growth factors o Study their biology & examining the genes o Purpose- understanding how animals in general are made and how their cells work CHAPTER 2 General info.:  Living organisms are made of Hydrogen, Carbon, Oxygen, and Nitrogen which is 96% of an organisms’ weight  Atoms with more than 4 outermost shell are rare  Atoms with complete outer shell are stable and chemically unreactive  Atoms with incomplete outer shell have a strong tendency to interact with other atoms either by gaining or losing electrons to become stable  Metals have an incomplete outer shell  Inert gases have a full outer shell Chemical Bonds:  Ionic Bonds o When electrons (-) are donated by 1 atom to another o Formed between atoms by losing (donating) or gaining (accepting) an electron o Ionic Bonds are called salts because both atoms become electrically charged ions o For example, Na and Cl atom. Na lost an electron. Cl gained an electron. Now they turn in ???????? and ???????? .  Covalent Bonds o When 2 atoms share a pair of electrons o The shared electrons (-) form a cloud of negative charge that is densest between the 2 positively charged nuclei o The attraction and repulsion forces are balances having the partially positively charged atoms at the end and the atom in the middle is partially negative. For example, H20. o Covalent bonds are STRONG and can be broken only during specific chemical reactions controlled by the enzymes  Noncovalent Bonds o The ionic bond that hold NaCl ions in a salt crystal is known as an electrostatic attraction o Electrostatic attraction strong on their own but weak in water o Strongest when the atoms involved are fully charged o It is considered a weak bond o Weak electrostatic attraction between molecules that are polar covalent bonds o Strong attraction between 2 molecules when they fit closely together o This binding makes proteins possible to function as enzymes  Hydrogen Bonds o Example: H20 o Highly polar since Oxygen is strongly attractive for electrons but Hydrogen is only weakly attractive. o The electrical attraction makes a weak bond called a hydrogen bond o Much weaker than covalent bonds o Easily broken by thermal motions o Important in the folding of a polypeptide chain and holding together the double stands of DNA  Van Der Waals Attractions o A form of attraction caused by fluctuating electric charges when 2 atoms comes together at a short distance o Weaker than Hydrogen Bonds  Hydrophobic interactions o A noncovalent interaction/bonds o Holds together the phosolipid molecules in the cell membranes Covalent BondsTypes of Bonds:  Single bond o Sharing of 2 electrons o Allowing rotation  Double bonds o Sharing of 2 pairs of electrons o Shorter and stronger than single bonds o Prevents rotation o Makes the bond rigid & less flexible arrangements of atoms  Polar bond o the electrons are shared unequally o Covalent bond between O & H or between N & H is polar o O & N attract electrons relatively strong o H atoms attract relatively weak o Polar covalent bond allows molecules to interact through electrical forces  Nonpolar bond o The electrons are shared equally o C & H attract each other equally which is nonpolar Lipid Bilayer:  Composed of hydrophobic and hydrophilic molecules creating an amphipathic structure  Hydrophobic: o “Water-fearing” o Uncharged o Form few or no hydrogen bonds o Doesn’t dissolve in water  Hydrophilic: o “Water-loving” o Includes sugars, DNA, RNA, and majority of proteins  Hydrocarbon: o H atoms are covalently lined to Carbon which is a nonpolar bond o Lipids do not dissolve in H20 which form thin membrane barriers Acid: +  Releases protons when dissolved in water forming ????3????  The higher the concentration of ????3???? the more acidic the solution  Pure H2O has a ph=7.0 which is neutral  Strong acids o Such as HCI lose their protons easily  Weak acids o Such as acetic acid holds on to protons more tightly when dissolve in water + o It will give up their protons more easily if the ???? concentration is low and will accept it back if the concentration is high Base:  Accepts a proton when dissolved in water  Strong base o Strong bases dissolve in water creating ions o Example, when NaOH dissociates into an aqueous solution to form Na and OH ions  Weak base o Weak tendency in accepting a proton from a water molecule Buffer:  Mixtures of weak acids & bases  Able to adjust protons concentration to ph=7 by releasing protons (acids) or taking them up (bases) Small Macromolecules in cells:  Organic molecules o Small & large carbon compounds made by cells  Inorganic molecules o All other molecules including H2O  Small organic molecules: o Sugars Polysaccharides, glycogen, & starch o Fatty acids Fats & membrane lipids o Amino acids Proteins o Nucleotides Larger organic molecules of the cell  Isomers: sets of molecules with the same chemical formula but different structures  Conformations: unlimited numbers of shapes Sugars:  Sugars Simplest sugar – the monosaccharides are compounds  Sugar and the larger molecules are made from carbohydrates  C, H, and O can join together by covalent bonds creating different shape structures  Monosaccharides can be linked by covalent bonds which can be referred to the glycosidic bonds o 2 monosaccharides – disaccharide o A polysaccharide can have thousands of monosaccharide units  Monomers: molecules made of small number such as 2 to 10.  Polymers: can contain hundreds or thousands of subunits Fatty Acids:  One is a long hydrocarbon (Hydrophobic and not very reactive)  A carboxyl group behaves like an acid get ionized which is chemically reactive and hydrophilic  Fatty acids covalently linked by the carboxylic acid  Hydrocarbon tail is saturated (No double bonds) which contains maximum numbers of hydrogen  Unsaturated tails: 1 or more double bonds  Double bonds between Carbon atoms creates a kink in the hydrocarbon tail  Fatty Acids can be broken down to produce 6 times more usable energy  Stored in the cytoplasm of many cells in the form of fat droplets Amino acids:  Used to build proteins  Contains a carboxylic acid group and amino group  Peptide bond (Formed by condensation reaction): covalent bond between 2 adjacent amino acids in a protein chain  Polypeptide: contains an amino group at one end (N-terminus) and a carboxyl group at the other end (C-terminus)  20 different amino acids found in all proteins  Some amino acids are: o Polar & hydrophilic o Nonpolar & hydrophobic Nucleotides:  Made of a Nitrogen ring compound linked to a 5-carbon sugar with either ribose or deoxyribose  A role in the storage & retrieval of biological unit  Long polymers which nucleotide subunits are linked together  Serve as building blocks of nucleic acids  Nucleosides containing 1 or more phosphate group attached to the sugar (2 main forms): o Ribonucleotides (contain ribose)  Single-stranded  Contains the bases; A, G, C, & U  Usually a more transient carrier of molecular instructions o Deoxy ribonucleotides (contain deoxyribose)  Double-stranded  Contains the bases: A, G, C, & T  Double helix made of 2 polynucleotide chains running in opposite directions held by hydrogen bonds  More stable  Hydrogen bonded helices  Acts as a long term repository for hereditary information o DNA & RNA linear sequence encodes genetic information o The bases are able to recognize & pair each other by Hydrogen bonding referred as base-pairing (Example, GC and AT or U  Nucleotide bases pyrimidines: Cytosine (C), Thymine (T), & Uracil (U)  Guanine (G) and Adenine (A)= purines Types of Reactions:  Condensation Reaction: Water is removed and a subunit is added creating a larger molecule  Hydrolysis Reaction: Water molecule is added and removes a subunit creating a smaller molecule


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