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BSC 300, Study Guide

by: Ashley Bartolomeo

BSC 300, Study Guide BSC 300

Ashley Bartolomeo
GPA 3.9

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Study guide on test number 1
Cell Biology
John yoder
Study Guide
50 ?




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This 9 page Study Guide was uploaded by Ashley Bartolomeo on Thursday September 8, 2016. The Study Guide belongs to BSC 300 at University of Alabama - Tuscaloosa taught by John yoder in Fall 2016. Since its upload, it has received 115 views. For similar materials see Cell Biology in Biology at University of Alabama - Tuscaloosa.


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Date Created: 09/08/16
Exam 1 Study Guide Chapter 1  Cells are the fundamental units of life The Cell Theory  All organisms are composed of one or more cells  The cell is the structural unit of life for all organisms  Cells can arise only by division from a preexisting cell Properties of living cells  Cells are the smallest units to exhibit the property of life o Evidence: plant or animal cells can be removed from the organism and cultured in the laboratory  Cells are highly complex and organized o Light microscope and electron microscope allow visualization of cellular infrastructure  Cells possess and can use their genetic program  Cells are capable of reproducing  Cells can acquire and utilize energy  Cells carry out chemical reactions o The sum total of chemical reactions in a cell represent that cell’s metabolism o All chemical reactions require enzymes  Cells engage in mechanical activities  Cells can respond to stimuli  Cells can self regulate o Evidence: experiment of Hans Driesch, German embryologist Similarities and Differences Between Prokaryotic and Eukaryotic Cells  Prokaryotes include bacteria and archaea  Eukaryotes include protists, animals, plants and fungi Similarities  Plasma membrane: similar in construction and composition  Genetic information: encoded in DNA/chromosomes using the same nucleotide molecules  Transcription and translation: similar mechanisms for synthesizing proteins  Metabolic pathways: many deeply conserved (ancient) pathways for acquiring and utilizing energy Differences  Complexity: prokaryotes are relatively simple; eukaryotes are more complex in structure and function  Cytoplasm vs cytosol: prokaryote cells are filled with cytosol: a gel-like liquid with dissolved ions and molecules. Eukaryotic cytoplasm is composed of the cytosol and the embedded membrane bound organelles which compartmentalize the cytosol providing greater regulation and diversity of metabolic activities  Cellular reproduction: eukaryotes divide by mitosis; prokaryotes divide by simple fission  Locomotion: eukaryotes use cytoplasmic movement, cilia and flagella. Prokaryotes have flagella, but they evolved separately and differ in both form and mechanism  Genetic material – packaging: o Prokaryote DNA is circular and localized to the nucleoid region with little associated protein o Eukaryotes have a membrane bound nucleus that controls molecular traffic. This allows tight regulate of gene expression. Eukaryotic DNA is highly associated with regulatory proteins (together called chromatin) that control packaging and gene expression  Genetic material – amount: o Eukaryotes have much more than prokaryotes o Prokaryote genomes range in size from 500,000 base pair to 10 million bp o Eukaryote genomes range from 100 million to 100 billion bp Stem Cells  Stem cells are undifferentiated cells capable of self-renewal and differentiation into diverse cell types  Adult stem cells have limited differentiation capacity and can differentiate into only a few types of closely related cells  Embryonic stem (ES) cells have even greater potential for differentiation than adult stem cells (they are pluripotent)  Induced pluripotent (iPS) stem cells: expression of just 4 genes is sufficient to transform fully differentiated cells into a pluripotent state o They then can be transformed into any cell type Endosymbiont Theory  Eukaryotic organelles evolved from intracellular prokaryotic parasites  Evidence supporting the endosymbiont theory o Mitochondira and chloroplasts duplicate independently of the nucleus o Organelles of eukaryotic cells contain their own circular chromosomes o Contain their own genes for ribosomal RNAs – more similar to prokaryotes’ than nuclear rRNA Chapter 2  Form drives function Covalent Bonds  Covalent bonds: electron pairs are shared between two atoms  Electrons in covalent bonds stay closest to the nucleus with the highest electronegativity: the tendency of an atom, or functional group to attract toward itself  Polar: asymmetric distributions of electrical charge due to unbalanced electronegativity  Nonpolar: lack asymmetric bonds  Oxygen, nitrogen and sulfur are strongly electronegative Noncovalent Bonds  Ionic bonds: attraction between charged atoms (ions)  Hydrogen bonds: polar H attracts electrons of a second polar bond (F,O,N)  Hydrophobic interactions: nonpolar molecules or regions of a molecule associate to minimize their exposure to polar molecules like water  Van der Waals forces: attraction between nonpolar molecule due to dipole formation All aspects of the unique structure and life supporting properties of water o Highly asymmetric molecule o Two covalent bonds highly polarized o All three atoms adept at forming hydrogen bonds o Excellent solvent (dissolves solutes in cell) o Can form hydrogen bonds with polar organic molecules o High heat capacity o Metabolism Structure and function of the three macromolecules studied thus far  Lipids  Carbohydrates o Disaccharides and polysaccharides have glycosidic bonds  Nucleic Acids The Nature of Biological Molecules  Hydrocarbons: only contain carbon and hydrogen o Hydrophobic and has no asymmetric charge distribution  Functional groups: groups of atoms within biochemical that provide specific characteristics and chemical properties Important Linkages  Ester bonds: forms between carboxylic acids and alcohol  Amide bond: between carboxylic acids and amines. Important peptide bonds that build proteins from amino acids Carbohydrates  Simple sugars  Energy storage and structural molecules  Simple sugars are monomers, aka monosaccharaides which are polymerized to polysaccharides  Depending on position of carbonyl group, monosaccharides are either: o Ketoses: carbonyl (C=O) on an internal carbon o Aldoses: carbonyl on a terminal carbon Lipids  Diverse group of molecules that are predominantly nonpolar  Saturated fats lack C=C double bonds  Unsaturated fats have one or more double bond Amino Acids  Peptide bonds join amino acids  Differ in the side chain (aka R group)  R groups may be polar charged, polar uncharged or nonpolar Polar Charged- side groups act as either weak organic acids or weak bases at cellular pH Polar Uncharged- R groups weakly acidic or basic; not fully charged at cellular pH Nonpolar- R groups hydrophobic; lack O and N Side Chains with Unique Properties 1. Glycine- small R group makes backbone flexible 2. Proline- R group forms ring with amino group 3. Cysteine- R group has reactive –SH Structure of Proteins Primary- specific linear sequence of amino acids joined by covalent peptide bonds Secondary- 3D arrangement of atoms to maximize the number of hydrogen bonds between neighboring amino acids Tertiary- conformation of the entire polypeptide, stabilized by a wide array of noncovalent bonds Quaternary: structure of proteins composed of subunits Nucleic Acids  Deoxyribonucleic acid (DNA) holds genetic information in all cellular organisms  Ribonucleic acid (RNA) is genetic material in some viruses, and In cells principally sever to transmit genetic information for protein translation  Each nucleotide consists of three parts: o A five carbon sugar o A C-5’ bound phosphate group o A C-1’ bound nitrogenous base  Adenine, guanine, cytosine, thymine and uracil o Bases are either purines (2 rings) which are adenine and guanine or pyrimidines (single ring) which are cytosine, uracil and thymine Chapter 3  Bioenergetics: study of energy transformations that occur in living organisms  Principle laws of thermodynamics governing cellular processes, including concepts of the system and surrounds o First law:  Cells are capable of energy transduction  Cells can neither be created now destroyed, only transferred or transformed o Second law: The degree of disorder (entropy) in the universe can only increase  Systems will change spontaneously towards arrangements with greater entropy  Gain in disorder and loss of available energy is = T∆S  Living cells can decrease their own energy by increasing the entropy of their environment  Macromolecules and storage molecules are broken down  increase in entropy  Macromolecules are synthesized and stored  decrease in entropy  The concept of free energy (G) and its relationship to the spontaneity of chemical processes, including metabolic reactions, and coupled endergonic/exergonic reactions o The value of G is of interest only when a system (such as a cell) undergoes a change (∆G), which is the amount of energy available to do work o ∆G=∆H-T∆S  H= Enthalpy (total energy content of system)  T= Absolute temperature (K)  S= Entropy  Thermodynamically favored (exergonic)  negative ∆G  Thermodynamically unfavored (endergonic)  positive ∆G o ∆G 0  Describes the free energy released when reactants are converted to o products under standard conditions [25 C, 1 atm, reactant/product -7 concentration0 1M, water 55.6M, pH 7=H+ ion concentration at 10 M]  Negative ∆G  spontaneous reaction C ][D] o ∆ G=∆G 0+RT log [ ]B]  Catabolic pathways break down molecules into smaller units and release energy through the cleavage of covalent bonds  Anabolic pathways construct molecules from smaller unites and require energy in order to form new covalent bonds  Keq can predict the favored direction of a reaction with known solute concentrations o Keq > 1: forward reaction favored o Keq < 1: reverse reaction favored Enzymes as Biological Catalysts  Enzymes: protein catalysts that increase the rate of chemical reactions  Catalysts: lower activation energy  Enzymes: o Work at cell-specific temperature and pH o Are highly specific for their substrates o Required in small amounts o Not consumed or altered irreversibly by the reaction o Have no effect on the thermodynamics of the reaction  Cofactors: inorganic atoms or molecules  Coenzymes: organic enzyme conjugates  Activation energy (Ea): required for any chemical reaction. Ea is the barrier that inhibits formation of a thermodynamically unstable intermediate  Substrates bind to active site and form enzyme-substrate complex  Interaction with substrate causes an induced fit  Kinetics: the study of rates of enzymatic reactions under various experimental conditions  Vmax, Maximal Velocity: is enzyme concentration dependent, but is used to determine the turnover number (aka catalytic constant) – the number of reactions catalyzed by a single enzyme per second  Enzymes with a low Km have a high affinity for their substrate  Enzyme with a high Km, have a poor affinity for their substrate  Lineweaver-Burke plot: shows Vmax and Km o Slope = Km/Vmax o 1/Vmax = Y-intercept o -1/Km = X-intercept  Km is a measure of how quickly an enzyme becomes saturated  Enzyme inhibitors slow the rate of enzymatic reactions  Three categories o Competitive – resemble substrate in structure; Vmax unaffected; Km increased o Non competitive - bind to sties other than active site and inactivate enzyme; alters enzyme conformation; Vmax cant be reached; Km is unchanged o Uncompetitive – bind only to enzyme substrate complex; decrease Vmax; Decrease Km  Phosphorylation o Transfer of a phosphate group from ATP, GTP or another molecule is termed phosphorylation o Reactions are catalyzed by enzymes called protein kinases o May alter protein conformation and can lead to activation or inactivation of enzyme function Chapter 18 Microscopy  Robert Hooke first observed and named cells in 1655 using a compound microscope with a magnification of 50x  Anton van Leeuwenhoek used a simpler microscope, increased magnification to 250x and discovered protists  Compound light microscopes o Condenser lens: focuses light o Objective lens: magnifies and establishes resolution o Ocular lens: empty magnification  Resolution: shortest distance between two points on a specimen that can be distinguished as separate entities  Resolution power of any objective is a function of the wave length of light and a value called the numerical aperture (NA) – specific for each lens  Resolution is a function of NA and  (wavelength)  d= _____0.61 x ___ NA o D = distance  NA = n x sin o N = refractive index o  = the half angle of scatter between the focused sample and objective lens  Shorter the focal distance, the grater the   Contrast: enhancing visibility  Bright-field microscopy: simplest form of optical microscopy  Phase-contrast microscopes make highly transparent objects more visible by converting differences in light refraction of some parts of the specimen into differences in light intensity  Differential Interference Contrast (DIC) optics gives a 3D quality to the image Light Microscope  Fluorescence microscopy uses fluorochromes: compounds that absorb one wavelength of light and emit a longer wavelength Transmission Electron Microscope (TEMs)  Uses electrons instead of light to form images Scanning Electron Microscope (SEMs)  Samples must be dehydrated and coated with layers of carbon or gold Atomic Force Microscopy  1000x higher resolution than light microscopy  Samples do not have to be fixed


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