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Molecular Biology 5 Description Biology 110681, 2005-2006, Trimester 2, 11th-12th grade BCA with Dr. Don DeWitt (v4 as of  2/22/06) Days: T & F; Mods: 22-24; Room 242 Return to Mol Bio 5 non-printing Description (i.e.,where you just came from) Return to Mol Bio 5 Handouts Page Course Overview: Why Mol Bio 5? The addition of this course is a result of shadowing students in college biology programs who have recently graduated from BCA. The topics covered in Mol. Bio. 5 focus on difficult material which I feel should be introduced at BCA in order to minimize the discomfort that may come if a student is required to wrestle with these topics for a first time in college. Mol. Bio. 5 is open to anyone a) who has taken Mol. Bio. 3 or has completed b) Anatomy and Physiology 1, c) Anatomy and Physiology (trimester 1) or d) Biological Chemistry with Dr. DeWitt. Overview The Life and Death of Proteins The topics of interest are related to the world of proteins with special focus on under-appreciated organelles (at BCA) or new information about familiar organelles: Where does RNA come from?  What is a gene? What is transcription? What is the structure of a ribosome? three-dimensional structure ribosomes as ribozymes What is translation? What factors determine how long mRNA can be used? mRNA degradation: exosomes / degradosomes What modifications can occur to a protein before use? proteolysis glycosylation phosphorylation What factors determine where a ribosome's product will go? the nuclear membrane / rough ER / Golgi connection secretory vesicles (exocytosis) lysosomes free ribosome products nucleoplasmic proteins histones DNA polymerase RNA polymerase cytoplasmic proteins amino acid deaminases organelle proteins chloroplasts Calvin cycle enzymes ATP synthase proteins mitochondria Krebs cycle enzymes Electron transport proteins ATP synthase proteins peroxisomes myofibrils actin myosin What factors determine how long an intracellular protein will be active? lysosomes proteasomes This material is found in the Cell Biology text  (chapters 7 & 14) as well as classroom presentations by the instructor and fellow students.  Each student uses these information sources to answer a series of in-class and take-home assessments.  The orientation of this course is a simulation of a college course.  Class note-taking skills are emphasized. Responsibility beyond the classroom is required. One research paper and one teaching presentation are assigned during this trimester.  Three current events reviews are also expected.  There are one in-class assessment. Student Objectives: Upon the successful completion of the study of Molecular Biology 4 the student will be able to describe the details and the role of: The Life and Death of Proteins Proteins Inside and Outside the Cell THE IDEA OF A PROTEIN STORED IN DNA Where the idea lives:  genes on chromosomes Chromosomes are found in prokaryotes, chlorplasts and mitochondria, and some viruses in circular form eukaryotes in linear form  are found in cells of prokaryotes in the cytoplasm eukaryotes in the nucleus mitochondrial matrix chloroplast stroma have a structure including a: circular form made from double stranded DNA single stranded DNA linear form made from double stranded DNA along with histone proteins which are used to supercoil the DNA into chromosomes single stranded DNA (viruses) single stranded RNA (viruses) double stranded RNA (viruses) vary in number between species such as 23 chromosomes in duplicate in humans, and 24 chromosomes in duplicate in chimpanzees, (REF) and are named by length of metaphase chromosome shown in a karyotype (see Figures at the right.) stay constant in number between normal members of the same species. An online karyotyping exercise is available. More details about banding patterns in chromosomes: CLASSIFICATION,  KARYOTYPING,  BANDING, and IDIOGRAMS. Where the idea for a protein lives:  genes are sections of chains of nucleotides called nucleic acids Nucleic acids are found in nature as polymers of monophosphate nucleotides held together between 5' carbons on one nucleotide and the 3' carbon of the adjacent nucleotide via a bond known as a phosphodiester bond. Nucleotides are three-component molecules known combinations of a) one sugar,  either ribose, or deoxyribose, and b) one nitrogenous base, either purines, or adenine, or guanine pyrimidines, and cytosine, or thymine, or uracil c) one or more phosphates, or two-component molecules known combinations of a) one nucleoside, which is one sugar bonded to one nitrogenous base, such as with ribose: adenosine guanosine cytidine uridine with deoxyribose deoxyadenosine deoxyguanosine deoxycytidine deoxythymidine b) one or more phosphates Nucleotide examples are ribose based found in RNA adenosine monophosphate (AMP) guanosine monophosphate (GMP) cytosine monophosphate (CMP) uridine monophosphate (UMP) deoxyribose based are found in DNA deoxyadenosine monophosphate (dAMP) deoxyguanosine monophosphate (dGMP) deoxycytosine monophosphate (dCMP) thymidine monophosphate (dTMP) A 3-page Summary of Nucleotides is available: Nucleotides Nucleotides are also used alone or in modified double nucleotides such as: single (ribose based): ATP ADP AMP GTP GDP GMP UTP UDP UMP ITP (using base inosine) IDP IMP cyclicAMP (cAMP) cyclicGMP (cGMP) coenzymeA double (ribose based) NAD+ NADH NADP+ NADPH FAD FADH2 There are two types of nucleic acids known as deoxyribonucleic acid (DNA), which is a polymer of monophosphate deoxyribonucleotides (MdRNs) such as: dAMP (abbrev: A) dGMP (abbrev: G) dTMP (abbrev: T) dCMP (abbrev: C) and is found in eukaryotic nuclei with a  double-stranded structure, with each strand arranged so that the structure of double stranded DNA is "anti-parallel" where the "parallel" aspect comes from the fact that opposite DNA strands are equidistant all along the molecule. This occurs because opposite strand bases are arranged with one purine (single ring) with a pyrimidine (double ring) so that opposite strands are approximately 3 base rings appart all along the DNA molecule. the "anti" aspect comes  from the fact that opposite strands run in opposite directions 3'-5' and 5'-3' and the double stranded DNA is twisted into a helix which gives DNA its "double helix" name and one DNA molecule is found in each chromosome. ribonucleic acid (RNA) ,  which is a polymer of monophosphate ribonucleotides (MrRNs) such as: AMP (abbrev: A) GMP (abbrev: G) UMP (abbrev: U) CMP (abbrev: C) and examples are; hnRNA, mRNA, tRNA, rRNA, snRNA The locations where DNA is found in cells are: the nucleus mitochondrial matrix (REF) chloroplast stroma RNA is found in cells are: the nucleus the cytoplasm mitochondrial matrix chloroplast stroma ribosomes The synthesis of nucleic acids such as: DNA is called DNA Synthesis or Duplication or Replication and occurs wherever the original DNA resided with the help of the enzyme DNA polymerase and building blocks triphosphate deoxyribonucleotides (TdRNs): dATP--> dAMP + PP dGTP--> dGMP + PP dTTP--> dTMP + PP dCTP--> dCMP + PP which are used to make polymers of monophosphate deoxyribonucleotides (MdRNs) using: dAMP     (abbrev: A) dGMP     (abbrev: G) dTMP     (abbrev: U) dCMP     (abbrev: C) Animation Overview for DNA duplication  ANIMATION RNA is called RNA Synthesis or Transcription and occurs wherever the  DNA which contains the gene being transcribed resided. The following section is a review of genes and transcription. Where the idea for a protein lives: the gene Genes carry a set of information for the synthesis of various RNAs via the process known as transcription. Various processes complete the task of producing a final functional product as shown below: Eukaryotic Protein Synthesis DNA gene --> transcription in nucleus --> hnRNA (a.k.a. primary transcript) (w/ introns & exons) hnRNA (w/ introns & exons) --> post-transcriptional processing in nucleus --> mRNA(w/exons) + introns mRNA (w/exons) --> translation at ribosomes --> polypeptide polypeptide --> post-translational processing in cytoplasm or RER & Golgi --> functional protein - Eukaryotic tRNA or rRNA or snRNA Synthesis DNA gene --> transcription in nucleoplasm --> tRNA or snRNA DNA gene --> transcription in nucleolus --> rRNA tRNA --> addition of amino acids in cytoplasm --> tRNA-amino acid rRNA --> combination with ribosomal proteins in nucleoplasm --> small & large ribosome subunits snRNA --> combination with proteins in nucleoplasm --> snRNPs --> spliceosomes Prokaryotic Protein Synthesis DNA gene --> transcription in cytoplasm --> mRNA mRNA --> translation at ribosomes --> polypeptide polypeptide --> post-translational processing in cytoplasm --> functional protein - Eukaryotic tRNA or rRNA Synthesis DNA gene --> transcription in cytoplasm -->  tRNA or rRNA tRNA --> addition of amino acids in cytoplasm --> tRNA-amino acid rRNA --> combination with ribosomal proteins in cytoplasm --> small & large ribosome subunits EXPRESSING THE IDEA OF A PROTEIN STORED IN DNA The decision to produce a RNA Some genes are always on and being expressed Other genes can be turned on or off depending on the needs of the cell of directions from outside the cell.  Some genes are permanently turned off after being used during early life, or vice versa.  Finally some genes are permanently turned off because the are used in a different cell type and not needed in the cell within which they reside.  For instance, the genes that dictate toe cellness, are not needed in cells that need to be heart cells. Whenever a gene's product is needed, its information must be accessed and the information must be copied into some type of RNA. TRANSCRIPTION: the process of making RNA: Transcription is the process of synthesizing a polymer of monophosphate ribonucleotides in a molecule known as RNA (the transcript) by copying (transcribing) the information in a DNA gene. What exactly is a GENE? Because a strand of DNA has 1000s of nucleotides, and smaller sections are genes, how does the transcription system know where a gene is?  Specifically,... which strand of DNA it is located on? where does it start? where does it end? An introductory view of a gene is that it STARTS wherever the nucleotide trio TAC is found while reading the DNA from 3' end to 5' end. ENDS wherever the nucleotide trios ATT, ATC, or ACT are found while reading the DNA from 3' end to 5' end. includes all the nucleotides from the START trio to the END trio.  Note that the END trios are also called STOP triplets. An introductory view of transcription is to synthesize a complementary copy of the gene into RNA using an enzyme called RNA Polymerase. But... as you may have figured out by now, Biology is usually more complicated, and nothing much is simple!  Prokaryotic transcription is less complicated than eukaryotic, and so prokaryotic transcription is a good place to dive into the details, beyond introductory views. RNA Polymerase enzyme does not look for  just TAC as the START location.  It uses information to the left of TAC which is called the UPSTREAM area.  (Note that everything after the first nucleotide T, is considered to be the DOWNSTREAM are of a gene.  Because there are mulitiple components of a gene, the idea of a TRANSCRIPTION UNIT has been developed. A Prokaryotic TRANSCRIPTION UNIT contains: Upstream DNA nucleotide sequences are the PROMOTER REGION used to bind the RNA polymerase enzyme and to provide a beginning to mRNA that allows for binding of mRNA to ribosomes. Downstream CODING REGION is the DNA nucleotide sequences from the Start site --> coding region <--Termination site TERMINATION REGION is the DNA nucleotide sequences that are important in the end-of-transcription step The RNA product is called the Primary Transcript: It can be: prokaryotes: messenger RNA (mRNA) ribosomal RNA (rRNA) transfer RNA (tRNA) eukaryotes: heteronuclear RNA (hnRNA) which becomes mRNA after introns are removed during post-transcriptional processing ribosomal RNA (rRNA) transfer RNA (tRNA) UNDER CONSTRUCTION.... Cistrons polycistronic: prokaryotes and chloroplasts monocistronic: eukaryotes INITIATION promoters all the DNA sequences containing binding sites for RNA polymerase and the transcription factors necessary for normal transcription on/off switches which side of the DNA to transcribe ELONGATION coding regions the Basal Transcription Apparatus used to synthesize RNA (REF) the transcribing enzyme protein RNA polymerase I in the nucleolus makes rRNA used to synthesize (along with other proteins) ribosomal subunits just small enough to move through nuclear envelope pores RNA polymerase II  in the nucleoplasm: makes hnRNA which becomes mRNA after introns are removed during post-transcriptional processing RNA polymerase III in the nucleoplasm and makes: tRNA used by ribosomes to carry amino acids to the translation machinery 5srRNA used to construct ribosomes small nuclear RNA (snRNA) used in small nuclear ribonucleoprotein particles (snRNPs) involved in the construction of splicesomes which are active with splicing hnRNA to remove introns in the production of eukaryotic mRNA transcription factor proteins Prokaryotes sigma factor Eukaryotes TFIID, TFIIA, TFIIB, TFIIE the building blocks: triphosphate ribonucleotides (TrRNs) provide energy via ATP--> AMP + PP UTP--> UMP + PP GTP--> GMP + PP CTP--> CMP + PP which are used to make polymers of monophosphate ribonucleotides (MrRNs) AMP (abbrev: A) GMP (abbrev: G) UMP (abbrev: U) CMP (abbrev: C) TERMINATION termination sequence Animation Overview for Transcription introductory details: ANIMATION 1 more details: ANIMATION 2 gene unwinding RIBOSOME STRUCTURE AND FUNCTION: (Refs: Class notes and Chapter 7) ribosomal biochemsitry: proteins and rRNA small subunit: home of mRNA large subunit: where the action is: E, P & A sites messenger RNA life and death the birth of a mRNA the real structure of mRNA translation of mRNA into a polypeptide degradosomes transfer RNA life and death the birth of a tRNA the life of tRNA the catalytic component: ribosomal proteins or RNA? LIFE AND DEATH AFTER TRANSLATION (Refs: Class notes and Chapter 12) the final maturation of proteins (aka, post-translational protein modifications) folding division into smaller proteins (proteolysis) insulin from proinsulin pepsin from pepsinogen glycosylation glycoproteins phosphorylation by ATP by inositol pyrophosphate (IP7 & IP8) protein kinases & cyclic AMP the life of proteins for use in the cytoplasm: enzymes hydrolases nucleases proteases synthases isomerases polymerases kinases phoshpatases oxido-reductases oxidases reductases dehydrogenases ATPases in myosin Na+/K+ pumps contractile events muscle actomyosin contraction non-muscle cell movement microtubules made from tubulin actin filaments made from actin motor proteins kinesins dyneins structural collagen elastin keratin fibroin storage hemoglobin myoglobin ovalbumin gluten casein ferritin nucleoplasm histones enzymes used in DNA duplication DNA polymerase used in RNA synthesis RNA polymerase inside organelles mitochondria enzymes used in the Krebs cycle lysosomes enzymes used in phagocytosis autophagy peroxisomes enzymes used in long chain fatty acid breakdown hydrogen peroxide degradation by catalase in or attached to membranes transporters used in the neuromuscular junction Na+/K+ ATPase Ca2+ pumps in presynaptic membranes sarcoplasmic reticulum H+ pumps in electron transport gastric mucosal cells Cl- pumps in postsynaptic membranes respiratory tract mucus secreting cells shuttles using facilitated diffusion GLUT presynaptic membrane Ca2+ uniport postsynaptic membrane Na+ , K+ and Cl- uniports neurotransmitter degradation acetylcholinesterase (AChE) the inner mitochondrial membrane ATP/ADP translocase H+ / Pi symport ATP synthase (a molecular motor) voltage gated ion transporters in axons and presynaptic membranes action potential stimulated Ca2+ transporter receptors ligand gated ion transporters neurotransmitters acetylcholine receptor GABA receptor protein hormone G-protein-coupled receptors energy receptors rhodopsin enzymes glycolytic in outer mitochondrial membrane guanylyl cyclase outside the cell hormones growth hormone insulin prolactin somatotropin digestive enzymes amylase trypsin pepsin lipase DNAase / RNAase transporters transferrin albumin antibodies life as an immunoglobulin THE DEATH OF PROTEINS IN lysosomes proteasomes Student Assignments: During the study of advanced protein processing and function, students will be given the opportunity to demonstrate their understanding of concepts by: writing a My Favorite Nobel Prize research paper --- Click here for DETAILS: NOBEL answering a Take-home PPAO on nucleotides, genes and muscle --- Click here for DETAILS: PPAO 1 answering a Take-home PPAO on various proteins --- Click here for DETAILS: PPAO 2a Click here for DETAILS: PPAO 2b presenting one complete lesson (in a group) during the trimester --- Click her for DETAILS: LESSON The percentage value of each assignment and its due date may be determined by clicking on the Assignment Due Dates arrow or the Assignment Details arrow below.  Formatting rules are available also. Additional Information: Textbook recources: We are using paper and electronic textbooks: Textbook 1 Essential Cell Biology: An Introduction to the Molecular Biology of the Cell. by  Bruce Alberts, Ph.D., Dennis Bray, PhD, Alexander Johnson, Ph.D., Julian Lewis, D. Phil., Martin Raff, M.D., Keith Roberts, Ph.D. and Peter Walter, Ph.D.  For information about them: AUTHORS The book is written especially for undergraduates in biological sciences, but its content can be easily understood and absorbed by advanced secondary school students who need a basic introduction to the essential topics in modern biology.Click on the book for more information from the publisher including the Table of Contents. Textbook 2 Another less useful resource, is Biology 6th ed. 2002  by  Neil Campbell and Jane Reece This book is a college level or AP level text book that is used by many colleges (and our AP Biology course) throughout the world for Introductory Biology courses. Electronic textbook resource: For Mol. Bio. 5, you will be responsible for chapters 3 and 4 which cover the chemistry and function of proteins. These chapters are available individually for downloading to your computer from the Mol. Bio. Download Center which may be accessed by clicking on the icons at the right.  They are also available on every Macintosh computer in room 242. These chapters can be viewed by using Adobe Persuasion on Mac or PC platforms. A Persuasion Player program must also be downloaded to run these chapters.  Persuasion is an older program that is similar in format to Microsoft's PowerPoint.  It was originally developed by Aldus but Adobe bought Aldus and then ceased development of Persuasion.  In the meantime, PowerPoint gained supremacy. Unfortunately there is no Persuasion-to- PowerPoint converter program so we continue to use Persuasion which still works on both platforms. Your electronic and paper textbooks and class notes are your major survival resources. Internet resources: A large table of internet links is available at: Mol Bio 5 Internet Return to Mol Bio 5 non-printing  Description (i.e.,where you just came from)