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BIL 255 Exam 1 - Study Guide - 7 Topics

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by: Allison

BIL 255 Exam 1 - Study Guide - 7 Topics BIL255

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These notes cover what will be on Exam 1.
Cell and Molecular Biology
Dr. Mallery and Dr. Diresta
Study Guide
Cellular and Molecular Biology, Biology, molecular biology
50 ?




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This 13 page Study Guide was uploaded by Allison on Thursday January 28, 2016. The Study Guide belongs to BIL255 at University of Miami taught by Dr. Mallery and Dr. Diresta in Fall. Since its upload, it has received 92 views. For similar materials see Cell and Molecular Biology in Biology at University of Miami.


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Date Created: 01/28/16
Cell Theory “All living things are made from cells.” Matthis Schleiden & Theodoore Schwann Bacteria Archaea Eukaryote Characteristics Predominantly multicellular NO YES NO Cell contains nucleus NO NO YES  C a DNA occurs in CIRCULAR form* YES YES NO r l Ribosome size 70s 70s 80s Capable of growth temperature  YES NO YES >80 d. C Operons present in DNA YES YES NO NO Introns present in most genes NO YES Capable of Methanogenesis NO YES NO * Eukaryote DNA is linear  ** Archaea membrane lipids are ether­ne  Methionine (isoprenoid)­linked lipids ester­used as   *** Bacteria, mitochondria & chloroplasts use N­formylmethionine cytosolic eukaryotes &  tRNA  Archaea do not use fMet, but ratYNY just MET.Initiator***   YYY Woese - Produced a tree with 3 Domains o Eubacteria – true bacteria o Archaea – ancient prokaryotes o Eukarya – modern eukaryotes  LUCA – Last Universal Common Ancestor – a single cell that lived 3 billion years ago from which ALL LIFE evolved from. This LUCA was founded by August Weismann.  Cell Theory replaced VITALISM – o Theory that living things cannot be explained only in terms of their physical & chemical nature. There is something non- material (a vital force) that makes them different than non-living things. Universal Characteristics of Cells 1. All cells store their heredity info in DNA 2. All cells REPLICATE their heredity info via same molecular mechanism – template polymerization 3. All cells replicate TRANSCRIBE heredity info into intermediate RNA via - template transcription 4. All cells translate RNA in same mechanistic way via CODON/ANTICODON “Chargaff” pairing using the same universal “genetic code” 5'  AUG  3' ­ mRNA A : T or A : U                     5' ­ tRNA                        ­fmet  G : C   5. All cells use protein catalysts (enzymes) to make or break covalent bonds E + S <---> ES <---> E + P 6. all cells regulate rate of gene transcription/translation, so only a portion of full repertoire of possible RNA's/proteins are copied, thus hereditary info dictates not only nature of cell's proteins, but also when/where they are to be made in a process known as, differential gene activity (in a time dependent fashion). 7. all cells metabolize - consume free energy to stay far away from chemical equilibrium. Consumption of free energy creates covalent bonds (which resist the disordering effects of thermal motion), as specified by hereditary info in a DNA sequence. The processes that cells have evolved to obtain free energy include: heterotrophy - oxidation of foods (via oxidation of covalent bonds) lithotrophy - chemical electron donors provide energy (H ,2H S2 S, Fe) autotrophy - capture of light energy via pigments (photosynthesis) N2& CO a2e stable and unreactive & reduction to NH & CH2O need2 energy. 8. all cells are enclosed in a spontaneously aggregating amphiphilic phospholipid bilayer: membranes regulate nutrient/water transfer, concentrate molecules internally, through embedded protein transport molecules.      Top 10 Characteristics of Cells 1. Have an evolutionary origin a. Via chemical evolution from LUCA 2. Highly complex a. You have a mix of biomolecules (C,O,H,N) cellular structural complexitity b. Structural complexity – figure 1.7 c. Typical animal plant cells – leads to two type of cells – prokaryotes & eukaryotic 3. Can replicate themselves – Mitosis & Meiosis 4. Acquire and use energy – via metabolic pathways – cells obey laws of chemistry & physics, laws of the universe a. Glycolysis b. Krebs c. ETC 5. Cells metabolize and are capable of 1000s reactions (via enzyme proteins) 6. Capable of self regulation – series of ordered reactions that are self adjusted a. Division growth, differentiation leads to cell form & function 7. Osmoregulation – control what get in/out of membranes (organelle or plasma) 8. Are Motile – involved in numerous mechanical activites including assembly, disassembly, movement of organelles, and motor proteins. 9. Respond to stimuli - via cell surface receptors (paracrine vs. endocrine) 10. Cells die – absence of life is a defining characteristic of living. CMB  The GOAL of CMB is to understand molecular basis of cell function and cellular processes.  Reductionist Approach – a complex can be “reduced” to simpler physical processes, to simplest level of physical explanation, where elementary particles interact within laws of physics.  Reductionism – primary experimental approach of CMB  CMB studies model organism – cheap, plentiful, reproducers with simple genomes & unique properties for research analysis. o Animals (Drosphilia melangaster) like zebrafish –  inch long tiny fish are helping scientists answer big questions on genetics & how diseases emerge.  embryos are clear, and they grow outside of the mother’s body  allow researchers to observe their development from the moment an egg is fertilized. In just two days, cells differentiate into separate organs, and the fish are capable of many actions – all available to view in real time under a microscope.  CMB studies Cells grown in Lab o Hela cells – immortal cell of human cervical cancer cells o Fibroblast cells – connective tissue that grows easily. o Immortal stem cells – stem cells have potential to become into different cell types in the body during early life. When a stem cell divides, each new cell has the potential either to remain a stem cell or become another type of cell with a more specialized function, such as a muscle cell, a red blood cell, or a brain cell. *The concept of trying to INTERPRET properties of living thing by a  detailed study of its CONSTITUENT MOLECULES and their  individual properties is referred to as?  Reductionism Allosteric Proteins It is thought that most protein molecules are allosteric. They can adopt two or more slightly  different conformations, and a shift from one to another caused by the binding of a ligand can  alter their activity.  Life Life is a chemical system FAR from equilibrium. It consumes free energy derived  from photosynthesis stored in  High energy bonds  Ionic concentration gradients  Couple reactions – reactions can be coupled if they share one or more intermediates. Overall free energy is sum of individual deltaG. A reaction not favored (+)deltaG.  Peptide Bonds A peptide bond is formed by condensation reaction an amino of one aa & carboxyl of another aa. *The peptide bond is shorter than a C=C but longer than a C­C, allows no free rotation of  groups attached to it and results in R­groups alternating in zig­zag fashion across length of a  polypeptide chain. T or F?  True Hydrogen Bonds Hydrogen Bond – a weak electrochemical attraction between 2 electronegative atoms.  Common structural motif of proteins in which linear sequence of amino acids folds into a  elongated structure and twists in corkscrew fashion?  A-helix = alpha helix o The first folding pattern to be discovered, called the α helix, was found in the protein α-keratin, which is abundant in skin and its derivatives— such as hair, nails Life Requires Autocatalysis  RNA world  existed on Earth before modern cells arose. According to this hypothesis, RNA  stored both genetic information and catalyzed the chemical reactions in primitive cells. Only  later in evolutionary time did DNA take over as the genetic material and proteins become the  major catalyst and structural component of cells. If this idea is correct, then the transition out of  the RNA world was never complete; as we have seen in this chapter, RNA still catalyzes several  fundamental reactions in modern­day cells, which can be viewed as molecular fossils of an  earlier world. What is evidence in favor of the RNA World Hypothesis?  RNA molecules have catalytic activity Peptide Bond A peptide bond. This covalent bond forms  when the carbon atom from the carboxyl  group of one amino acid shares electrons  with the nitrogen atom(blue) from the  amino group of a second amino acid. As  indicated, a molecule of water is lost in this condensation Which parts of the amino acid are involved  in peptide bonds?  The amino group on one amino  acid and carboxyl group on the  other. Globular Proteins Most of the proteins we have discussed so far are globular proteins, in which  the polypeptide chain folds up into a compact shape like a ball with an irregular surface.  Enzymes tend to be globular proteins: even though many are large and complicated, with  multiple subunits, most have an overall rounded shape. In a folded globular protein, the nonpolar (hydrophobic) amino acids tend to be..  Tucked away inside the protein Protein Kinase The different domains of a protein are often associated with different functions. Figure 3­ 12 shows an example—the Src protein kinase, which functions in signaling pathways inside  vertebrate cells (Src is pronounced “sarc”). This protein has four domains: the SH2 and SH3  domains have regulatory roles, while the two remaining domains are responsible for the kinase  catalytic activity. Later in the chapter, we shall return to this protein, in order to explain how  proteins can form molecular switches that transmit information throughout cells. *protein kinase ­ Enzyme that transfers the terminal phosphate group of ATP to a  specific amino acid of a target protein. Which of the following kinds of enzyme can add a phosphate group to another protein?  Kinase Allosteric Inhibitor Like proteins, RNAs can undergo allosteric conformational changes, either in response to small  molecules or to other RNAs. One artificially created ribozyme can exist in two entirely different  conformations, each with a different catalytic activity.        allosteric inhibi , an enzyme having a secondary active site called an allosteric site closes the active site, preventing the formation of  the enzyme­substrate complex. *ribozyme – RNA with catalytic activity How does an allosteric inhibitor affect the active site of an enzyme?  It binds to the second site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate Protein Families A protein family is a group of proteins that share a common evolutionary origin, reflected by  their related functions and similarities in sequence or structure. Protein families are often  arranged into hierarchies, with proteins that share a common ancestor subdivided into smaller,  more closely related groups. What are protein families?  Evolutionary related proteins that are similar in sequence, 3D conformation and function. All Proteins Bind to other Molecules The ability of a protein to bind selectively and with high affinity to a ligand depends on the  formation of a set of weak, noncovalent bonds *ligand ­ Any molecule that binds to a specific site on a protein or other molecule. The ability of a protein to bind selectively and with high affinity to a specific molecule is due to  which type of bonds?  Weak, noncovalent bonds Many weak bonds are needed  to enable a protein to bind  tightly to a second molecule,  The Bacteria – Staphylococcus  which is called a ligand for  appear purple back in color  the protein. A ligand must  upon which Gram Stain?  therefore fit precisely into a  protein’s binding site, like a   Gram Positive (+) hand into a glove, so that a  Medical Identification done  large number of noncovalent  through this.  Prokaryotes vs Eukaryotes PROKARYOTE ­ "pro" = before + "karyon"  Gk­ker= nucleus  includes archaea bacteria  &today's eubacteria  o including  blue green algae            includes members of the original Kingdom Monera (now  Domains Archaea & Eubacteria). Characteristics:   3 main cellular shapes* in prokaryotic cells:  cocci, bacilli, spirochetes image on right.  size range ­ 0.1 to 10 µm diameter  genes contain "naked DNA" ­, i.e., there are no "chromosomes "*     they lack significant internal membrane bound organelles have little internal  compartmentation  EUKARYOTIC:   “eu”­true   “karyon”­nucleus  cell plan of multi­cellular organisms  eukarya: includes the algae & protozoa, fungi & slime molds, &  all plants & animals,  Example ­ 4 of the 5 Kingdoms  o Protista o Fungi o Plantae o Animalia       CHARACTERISTIC of EUKARYOTES:  nucleus ­ 'may have been single greatest step in evolution of higher life forms '  genes in "chromosomes*" o colored bodies made of   DNA   histone proteins  karyotype*  chromosome locales*  chromosome activity via locale*  contains more DNA (1,000xmore) than  prokaryotes extensive internalmembranes ­ endomembrane system* (nuclear  memb + ER + Golgi + vesicles)  presence of more flexible cell "walls" allows endocytosis/phagocytosis*)  presence of organelles­ significant internal compartmentalization of function  o organelle ­ a subcell part that has a distinct metabolic function                       presence of cytoskeleton* o provides framework to be larger & provide form/shape  reproduce sexually  usually larger ­ cell volume 10X > than bacteria­size 5.0 to 20 µm diameter Cytoskeleton Fibroblast cells ­ cells of connective tissue that are responsible for extra­cellular  matrix and secreting connective tissue proteins, such as collagen. Fluorescent light micrograph of fibroblast cells, showing their nuclei (purple)  and cytoskeleton. The cytoskeleton is made up of microtubules of the  protein tubulin (yellow) and filaments of the protein actin (blue).  The cytoskeleton supports the cell's structure, allows the cell to move and assists in the transport of organelles and vesicles within the cell.  Magnification: x980 when printed 10cm wide. *Microtubules, microfilaments, and intermediate filaments are  components of the? o Cytoskeleton Light Microscope   Light Microscopes ­ optical microscopy involves the diffraction, refraction, or reflection of light (electromagnetic radiation) interacting with live or prepared samples & subsequent collection  of scattered radiation (light) to build up magnified images of small objects using compound  lens* =  [objective lens ­ magnifies object (150x)  & ocular lens (10x) = 1,500x magnification]  These systems exploit differences in the  way light travels through regions of a cell  with different refractive indexes.         Refractive Index = how light travels        thru a medium.  RF water of = 1.33       i.e., 1.33x slower than thru vacuum &   how much light is bent.  All these images   can be made with same microscope     mply by changing optical components.  Brightfield ­  light passes thru a specimen  with little contrast. A cell is 70% water &  is colorless & translucent.          Phase contrast ­ incident light is out of  phase with & transmitted light.  When iL  and tL phases are synchronized by an  interference lens good contrast results.           Differential­interference­contrast  i.e., Nomarski microscopy uses   interference between polarized light   that produces shadow casting images   giving pseudo­relief.             Cell Division via Nomarski          Darkfield ­ illuminating light is directed  from the side so only scattered light  All are types of lighto Fluorescence  enters the lens, thus cell appears lite microscopy except? o Dark field  against a dark background.    o Bright field o Phase contrast o All of the above Active site of an enzyme?  Found at center of globular enzymes. The smallest known cells are a group of tiny bacteria called   mycoplasms. RNA 2nd) Experimental approach:   build an artificial  MODEL  MOLECULAR  REPLICATIVE  SYSTEM          Argues for the emergence of RNA molecular replication as both an information­carrier molecule                                   and a catalytic molecule as an important 1st step...  Evolution of an RNA world...   1st proposed by Walter Gilbert in 1986                                  emanated from debate of which came 1st DNA or RNA?                                  early RNA may have done both functions: coding proteins & nucleic acid replications              Experiments to build replicative molecules:                                                                                    in 1989  Sidney Altman  &   Tom Cech ­ received Nobel Prize for demonstrating                                that RNA molecules (RIBOZYMES*) have CATALYTIC ACTIVITY                           i.e., these RNA's could catalyze polymeric cleavage in a sequence­specific way and                                          also might be capable of ligation of RNA fragments together...               maybe, if chains of RNA can be a template & also catalyze polymerization of like molecules,                      then RNA molecules might have been the 1st SELF­REPLICATING molecular entity 


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