Basic Principles of Transcription and Translation

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "Basic Principles of Transcription and Translation"

Transcription

1 The Flow of Genetic Information The information content of DNA is in the form of specific sequences of nucleotides The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins Proteins are the links between genotype and phenotype Gene expression, the process by which DNA directs protein synthesis, includes two stages: transcription and translation The ribosome is part of the cellular machinery for translation, polypeptide synthesis Basic Principles of Transcription and Translation RNA is the intermediate between genes and the proteins for which they code Transcription is the synthesis of RNA under the direction of DNA Transcription produces messenger RNA (mrna) Translation is the synthesis of a polypeptide, which occurs under the direction of mrna Ribosomes are the sites of translation

2 In prokaryotes, mrna produced by transcription is immediately translated without more processing In a eukaryotic cell, the nuclear envelope separates transcription from translation Eukaryotic RNA transcripts are modified through RNA processing to yield finished mrna A primary transcript is the initial RNA transcript from any gene The central dogma is the concept that cells are governed by a cellular chain of command: DNA RNA protein Eukaryotic RNA transcripts are modified through RNA processing to yield finished mrna TRANSCRIPTION TRANSLATION Polypeptide DNA mrna Ribosome a) Bacterial cell. In a bacterial cell which lacks a nucleus, mrna produced by transcription is immediately translated without additional processing. (a) Bacterial cell TRANSCRIPTION DNA Nuclear envelope b) Eukaryotic cell. The nucleus provides a separate compartment for transcription. The original RNA transcript called pre mrna is processed in various ways before leaving the nucleus as mrna. RNA PROCESSING Pre-mRNA mrna TRANSLATION Ribosome Polypeptide (b) Eukaryotic cell Overview: the roles of transcription and translation in the flow of genetic information. In a cell inherited information flows from DNA to RNA to protein. The two main stages of information flow are transcription and translation.

3 TRANSCRIPTION DNA mrna (a) Bacterial cell TRANSCRIPTION TRANSLATION Polypeptide DNA mrna Ribosome Nuclear envelope TRANSCRIPTION DNA Pre-mRNA (b) Eukaryotic cell

4 Nuclear envelope TRANSCRIPTION DNA RNA PROCESSING Pre-mRNA mrna (b) Eukaryotic cell Nuclear envelope TRANSCRIPTION DNA RNA PROCESSING Pre-mRNA mrna TRANSLATION Ribosome Polypeptide (b) Eukaryotic cell

5 The Genetic Code How are the instructions for assembling amino acids into proteins encoded into DNA? There are 20 amino acids, but there are only four nucleotide bases in DNA How many bases correspond to an amino acid? Codons: Triplets of Bases The flow of information from gene to protein is based on a triplet code: a series of nonoverlapping, three-nucleotide words These triplets are the smallest units of uniform length that can code for all the amino acids Example: AGT at a particular position on a DNA strand results in the placement of the amino acid serine at the corresponding position of the polypeptide to be produced

6 During transcription, one of the two DNA strands called the template strand provides a template for ordering the sequence of nucleotides in an RNA transcript During translation, the mrna base triplets, called codons, are read in the to direction Each codon specifies the amino acid to be placed at the corresponding position along a polypeptide Colons along an mrna molecule are read by translation machinery in the to direction Each codon specifies the addition of one of 20 amino acids DNA molecule Gene 1 Gene 2 DNA template strand TRANSCRIPTION mrna Codon TRANSLATION Protein Amino acid Gene 3 The triplet code. For each gene, one strand of DNA functions as a template for transcription. The base pairing rules for DNA synthesis also guide transcription, but uracil (U) takes the place of thymine (T) in RNA. During translation the mrna is read as a sequence of base triplets called codons. Each codon specifies an amino acid to be added to the growing polypeptide chain. The mrna is read in the 5 3 direction.

7 Cracking the Code All 64 codons were deciphered by the mid-1960s Of the 64 triplets, 61 code for amino acids; 3 triplets are stop signals to end translation The genetic code is redundant but not ambiguous; no codon specifies more than one amino acid Codons must be read in the correct reading frame (correct groupings) in order for the specified polypeptide to be produced Second mrna base First mrna base ( end of codon) Third mrna base ( end of codon) The dictionary of the genetic code. The three bases of an mrna codon are designated here as the first, second and third bases reading in the 5 3 direction along the mrna. The codon AUG not only stands for the amino acid methionine (Met) but also functions as a start signal for ribosomes to begin translating the mrna at that point. Three of the 64 codons function as stop signals marking the end of a genetic message

8 Evolution of the Genetic Code The genetic code is nearly universal, shared by the simplest bacteria to the most complex animals Genes can be transcribed and translated after being transplanted from one species to another Because diverse forms of life share a common genetic code, one species can be programmed to produce proteins characteristic of a second species by introducing DNA from the second species into the first Transcription is the DNA-directed synthesis of RNA: a closer look Transcription, the first stage of gene expression, can be examined in more detail The three stages of transcription: Initiation Elongation Termination

9 Molecular Components of Transcription RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotides RNA synthesis follows the same base-pairing rules as DNA, except uracil substitutes for thymine The DNA sequence where RNA polymerase attaches is called the promoter; in bacteria, the sequence signaling the end of transcription is called the terminator The stretch of DNA that is transcribed is called a transcription unit Promoter Transcription unit DNA Start point RNA polymerase 1 Initiation Unwound DNA RNA transcript Template strand of DNA 2 Elongation Elongation Nontemplate strand of DNA RNA polymerase end RNA nucleotides Rewound DNA RNA transcript 3 Termination Completed RNA transcript Newly made RNA Direction of transcription ( downstream ) Template strand of DNA

10 Promoter Start point RNA polymerase Unwound DNA Rewound DNA RNA transcript Transcription unit RNA transcript DNA 1 Initiation Template strand of DNA 2 Elongation 3 Termination Completed RNA transcript 1) Initiation. After RNA polymerase binds to the promoter, the DNA strands unwind and the polymerase initiates RNA synthesis at the start point on the template strand. 2) 2) Elongation The polymerase moves downstream unwinding the DNA and elongating the RNA transcript 5 3 In the wake of transcription the DNA strands re-form a double helix. 3) 3) Termination Eventually the RNA transcript is released and the polymerase detaches from the DNA The stages of transcription: initiation elongation and termination. Thus general depiction of transcription applies to both bacteria and eukaryotes but the details of termination differ, as described in the text. Also in a bacterium the transcript is immediately usable as mrna in a eukaryote the RNA transcript must first undergo processing. Elongation Nontemplate strand of DNA RNA polymerase RNA nucleotides end Newly made RNA Direction of transcription ( downstream ) Template strand of DNA

11 RNA Polymerase Binding and Initiation of Transcription Promoters signal the initiation of RNA synthesis Transcription factors mediate the binding of RNA polymerase and the initiation of transcription The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes 1 Promoter Template TATA box Start point Template DNA strand Transcription factors RNA polymerase II 2 3 Transcription factors RNA transcript Transcription initiation complex 1) A eukaryotic promoter commonly includes a TATA box a nucleotide sequence containing TATA about 25 nucleotides upstream from the transcription start point. By convention nucleotide sequences are given as they occur on the nontemplate strand 2) Several transcription factors one recognizing the TATA box must bind to the DNA before RNA polymerase II can do so. 3) Additional transcription factors (purple) bind to the DNA along with RNA polymerase II forming the transcription initiation complex. The DNA double helix then unwinds and RNA synthesis begins at the start point on the template strand. The initiation of transcription at a eukaryotic promoter. In eukaryotic cells proteins called transcription factors mediate the initiation of transcription by RNA polymerase II

12 Elongation of the RNA Strand As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time Transcription progresses at a rate of 40 nucleotides per second in eukaryotes A gene can be transcribed simultaneously by several RNA polymerases Termination of Transcription The mechanisms of termination are different in bacteria and eukaryotes In bacteria, the polymerase stops transcription at the end of the terminator In eukaryotes, the polymerase continues transcription after the pre-mrna is cleaved from the growing RNA chain; the polymerase eventually falls off the DNA

13 Eukaryotic cells modify RNA after transcription Enzymes in the eukaryotic nucleus modify pre-mrna before the genetic messages are dispatched to the cytoplasm During RNA processing, both ends of the primary transcript are usually altered Also, usually some interior parts of the molecule are cut out, and the other parts spliced together Alteration of mrna Ends Each end of a pre-mrna molecule is modified in a particular way: The end receives a modified nucleotide cap The end gets a poly-a tail These modifications share several functions: They seem to facilitate the export of mrna They protect mrna from hydrolytic enzymes They help ribosomes attach to the end

14 Protein-coding segment Polyadenylation signal G P P P AAUAAA AAA AAA Cap UTR Start codon Stop codon UTR Poly-A tail RNA processing addition of the 5 cap and poly A tail. Enzymes modify the two ends of a eukaryotic pre mrna molecule. The modified ends may promote the export of mrna from the nucleus and they help protect the mrna from degradation. When the mrna reaches the cytoplasm the modified ends in conjunction with certain cytoplasmic proteins facilitate ribosome attachment. The 5 cap and poly A tail are not translated into protein, nor are the regions called the 5 untranslated regions (5 UTR) and 3 untranslated regions (3 UTR) Split Genes and RNA Splicing Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions These noncoding regions are called intervening sequences, or introns The other regions are called exons because they are eventually expressed, usually translated into amino acid sequences RNA splicing removes introns and joins exons, creating an mrna molecule with a continuous coding sequence

15 Exon Intron Exon Intron Pre-mRNA Cap Exon Poly-A tail 146 Coding segment Introns cut out and exons spliced together mrna Cap Poly-A tail UTR UTR RNA processing: mrna splicing. The RNA molecule shown here codes for β globin one of the polypeptides of hemoglobin. The numbers under the RNA refer to the codons. β globin is 146 amino acids long. The β globin gene and its pre mrna transcript have three exons corresponding to sequences that will leave the nucleus as RNA. (The 5 UTR and 3 UTR are parts of exons because they are included in the mrna however they do not code for protein). During RNA processing the introns are cut out and the exons are spliced together. In many genes the introns are much larger relative to the exons than they are in the β globin gene. The mrna is not drawn to scale. In some cases, RNA splicing is carried out by spliceosomes Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snrnps) that recognize the splice sites

16 Protein snrna RNA transcript (pre-mrna) Exon 1 Intron Exon 2 snrnps Spliceosome components Spliceosome mrna Exon 1 Exon 2 Other proteins Cut-out intron The roles of snrnps and spliceosomes in pre mrna splicing. The diagram shows only a portion of the pre mrna transcript, additional introns and exons lie downstream from the pictured ones here. 1) Small nuclear ribonucleoprotein (snrnps) and other proteins form a molecular complex called a spliceosome on a pre mrna molecules containing exons and introns. 2) Within the spliceosome snrna base pairs with nucleotides at specific sites along the intron. 3) The spliceosome cuts the pre mrna releasing the intron and at the same time splices the exons together. The spliceosome then comes apart releasing mrna which now contains only exons. Ribozymes Ribozymes are catalytic RNA molecules that function as enzymes and can splice RNA The discovery of ribozymes rendered obsolete the belief that all biological catalysts were proteins Three properties of RNA enable it to function as an enzyme It can form a three-dimensional structure because of its ability to base pair with itself Some bases in RNA contain functional groups RNA may hydrogen-bond with other nucleic acid molecules

17 The Functional and Evolutionary Importance of Introns Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA splicing Such variations are called alternative RNA splicing Because of alternative splicing, the number of different proteins an organism can produce is much greater than its number of genes Proteins often have a modular architecture consisting of discrete regions called domains In many cases, different exons code for the different domains in a protein Exon shuffling may result in the evolution of new proteins

18 DNA Gene Exon 1 Intron Exon 2 Intron Exon 3 Transcription RNA processing Translation Correspondence between exons and protein domains. Domain 3 Domain 2 Domain 1 Polypeptide Translation is the RNA-directed synthesis of a polypeptide: a closer look A cell translates an mrna message into protein with the help of transfer RNA (trna) Molecules of trna are not identical: Each carries a specific amino acid on one end Each has an anticodon on the other end; the anticodon base-pairs with a complementary codon on mrna

19 Polypeptide Trp Phe Ribosome Amino acids trna with amino acid attached Gly trna Anticodon Translation: the basic concept. As a molecule of mrna is moved through a ribosome codons are translated into amino acids one by one. The interpreters are trna molecules, each type with a specific anticodon at one end and a corresponding amino acid at the other end. A trna adds its amino acid cargo to a growing polypeptide chain when the anticodon hydrogen bonds to a complementary codon on the mrna. Codons mrna The Structure and Function of Transfer RNA A trna molecule consists of a single RNA strand that is only about 80 nucleotides long A C C Flattened into one plane to reveal its base pairing, a trna molecule looks like a cloverleaf Because of hydrogen bonds, trna actually twists and folds into a three-dimensional molecule trna is roughly L-shaped

20 Amino acid attachment site Anticodon (a) Two-dimensional structure Anticodon Hydrogen bonds Hydrogen bonds (b) Three-dimensional structure Amino acid attachment site Anticodon (c) Symbol used in this book Two dimensional structure. The four base paired regions and three loops are characteristic of all trnas as is the base sequence of the amino acid attachment site at the 3 end. The anticodon triplet is unique to each trna type as are some sequences in the other two loops. (the asterisks mark bases that have been chemically modified a characteristic of trna) The structure of transfer RNA (trna). Anticodons are conventionally written 3 5 to align properly with codons written 5 3. For base pairing RNA strands must be antiparallel like DNA. For example anticodon 3 AAG 5 pairs with mrna codon 5 UUC 3 Accurate translation requires two steps: First: a correct match between a trna and an amino acid, done by the enzyme aminoacyl-trna synthetase Second: a correct match between the trna anticodon and an mrna codon Flexible pairing at the third base of a codon is called wobble and allows some trnas to bind to more than one codon

21 Amino acid P P P ATP Adenosine Aminoacyl-tRNA synthetase (enzyme) 1) Active site binds to the amino acid and ATP 2) ATP loses two P groups and joins amino acids as AMP trna P Adenosine P P i P i P i trna Aminoacyl-tRNA synthetase 3) Appropriate trna covalently bonds to amino acid displacing AMP 4) The trna charged with amino acid is released by the enzyme P Adenosine AMP Aminoacyl-tRNA ( charged trna ) Computer model An aminoacyl trna synthethase joining a specific amino acid to a trna. Linkage of the trna and amino acid is an endergonic process that occurs at the expense of ATP. The ATP loses two phosphate groups becoming AMP (adenosine monophosphate) Ribosomes Ribosomes facilitate specific coupling of trna anticodons with mrna codons in protein synthesis The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rrna)

22 trna molecules Growing polypeptide E P A Exit tunnel Large subunit Small subunit mrna (a) Computer model of functioning ribosome P site (Peptidyl-tRNA binding site) E site (Exit site) mrna binding site E P A A site (AminoacyltRNA binding site) Large subunit Small subunit (b) Schematic model showing binding sites Amino end mrna E Codons Growing polypeptide Next amino acid to be added to polypeptide chain trna (c) Schematic model with mrna and trna a) Computer model of functioning ribosome. This is a model of a bacterial ribosome showing its overall shape. The eukaryotic ribosome is roughly similar. A ribosomal subunit is an aggregate of ribosomal RNA molecules and proteins b) Schematic model showing binding sites. A ribosome has an mrna binding site and three trna binding sites known as the A, P and E sites. c) Schematic model with mrna and trna. A trna fits into a binding site when its anticodon base pairs with an mrna codon. The P site holds the trna attached to the growing polypetide. The A site holds the trna carrying the next amino acid to be added to the polypeptide chain. Discharged trnas leaves from the E site. The anatomy of a functioning ribosome. A ribosome has three binding sites for trna: The P site holds the trna that carries the growing polypeptide chain The A site holds the trna that carries the next amino acid to be added to the chain The E site is the exit site, where discharged trnas leave the ribosome

23 Building a Polypeptide The three stages of translation: Initiation Elongation Termination All three stages require protein factors that aid in the translation process Ribosome Association and Initiation of Translation The initiation stage of translation brings together mrna, a trna with the first amino acid, and the two ribosomal subunits First, a small ribosomal subunit binds with mrna and a special initiator trna Then the small subunit moves along the mrna until it reaches the start codon (AUG) Proteins called initiation factors bring in the large subunit that completes the translation initiation complex

24 Met U A C A U G P site Met Large ribosomal subunit Initiator trna mrna Start codon mrna binding site GTP Small ribosomal subunit GDP E A Translation initiation complex 1) A small ribosomal subunit binds to a molecule of mrna. In a bacterial cell the mrna binding site on this subunit recognizes a specific nucleotide sequence on the mrna just upstream of the start codon. An initiator trna with the anticodon UAC base pairs with the start codon, AUG. This trna carries the amino acid methionine Met) 2) The arrival of a large ribosomal subunit completes the initiation complex. Proteins called initiation factors (not shown) are required to bring all the translation components together GTP provides the energy for the assembly. The initiator trna is in the P site, the A site is available to the trna bearing the next amino acid. The initiation of translation Elongation of the Polypeptide Chain During the elongation stage, amino acids are added one by one to the preceding amino acid Each addition involves proteins called elongation factors and occurs in three steps: codon recognition, peptide bond formation, and translocation

25 The elongation cycle of translation. The hydrolysis of GTP plays an important role in the elongation process Ribosome ready for next aminoacyl trna Amino end of polypeptide mrna E P site site A GTP 1) Codon recognition. The anticodon of an incoming aminoacyl trna base pairs with the complementary mrna codon in the A site. Hydrolysis of GTP increases the accuracy and efficiency of this step GDP E E P A P A 3) Translocation The ribosome translocates the trna in the A to the P site. The empty trna in the P site is moved to the E site where it is released. The mrna moves along with its bound trnas bringing the next codon to be translated into the A site GDP GTP E P A 2) Peptide bond formation. An rrna molecule of the large ribosomal subunit catalyses the formation of a peptide bond between the new amino acid in the A site and the carboxyl end of the growing polypeptide in the P site. This step removes the polypeptide from the trna in the P site and attaches it to the amino acid on the trna in the A site Termination of Translation Termination occurs when a stop codon in the mrna reaches the A site of the ribosome The A site accepts a protein called a release factor The release factor causes the addition of a water molecule instead of an amino acid This reaction releases the polypeptide, and the translation assembly then comes apart

26 Release factor Free polypeptide Stop codon (UAG, UAA, or UGA) When a ribosome reaches a stop codon on mrna, the A site of the ribosome accepts a release factor a protein shaped like a trna instead of an aminoacyl trna, The release factor hydrolyzes the bond between the trna in the P site and the last amino acid of the polypeptide chain. The polypeptide is thus freed from the ribosome. The two ribosomal subunits and the other components of the assembly dissociate. The termination of translation. Like elongation, termination requires GTP hydrolysis as well as additional factors which are not shown here Polyribosomes A number of ribosomes can translate a single mrna simultaneously, forming a polyribosome (or polysome) Polyribosomes enable a cell to make many copies of a polypeptide very quickly

27 Growing polypeptides Completed polypeptides Incoming ribosomal subunits Start of mrna ( end) Polyribosome End of mrna ( end) An mrna molecule is generally translated simultaneously by several ribosomes in clusters called polyribosomes. Ribosomes mrna 0.1 µm This micrograph shows a large polyribosome in a prokaryotic cell (TEM). Completing and Targeting the Functional Protein Often translation is not sufficient to make a functional protein Polypeptide chains are modified after translation Completed proteins are targeted to specific sites in the cell

28 Protein Folding and Post-Translational Modifications During and after synthesis, a polypeptide chain spontaneously coils and folds into its three-dimensional shape Proteins may also require post-translational modifications before doing their job Some polypeptides are activated by enzymes that cleave them Other polypeptides come together to form the subunits of a protein Targeting Polypeptides to Specific Locations Two populations of ribosomes are evident in cells: free ribsomes (in the cytosol) and bound ribosomes (attached to the ER) Free ribosomes mostly synthesize proteins that function in the cytosol Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell Ribosomes are identical and can switch from free to bound

29 Polypeptide synthesis always begins in the cytosol Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER Polypeptides destined for the ER or for secretion are marked by a signal peptide A signal-recognition particle (SRP) binds to the signal peptide The SRP brings the signal peptide and its ribosome to the ER 1) Polypetide synthesis begins on a free ribosomo in the cytosol. 2) An SRP binds to the signal peptide. halting synthesis momentarily 3) The SRP binds to a receptor protein in the ER membrane. This receptor is part of a protein complex (a translocation complex) that has a membrane pore and a signal cleaving enzyme 4) The SRP leaves and 5) The signal polypetides synthesis cleaving resumes with enzyme simultaneous cuts off the translocation across the signal membrane (The signal peptide peptide stays attached to the translocation complex) 6) The rest of the completed polypeptide leaves the ribosome and folds into its final conformation Ribosome Signal peptide Signalrecognition particle (SRP) CYTOSOL ER LUMEN mrna Translocation complex SRP receptor protein Signal peptide removed ER membrane Protein The signal mechanism for targeting proteins to the ER. A polypeptide destined for the endomembrane system or for secretion from the cell begins with a signal peptide a series of amino acids that targets it for the ER. This figure shows the synthesis of a secretory protein and its simultaneous import into the ER. In the ER and then in the Golgi, the protein will be processed further. Finally a transport vesicle will convey it to the plasma membrane for release from the cell

30 RNA plays multiple roles in the cell: a review Type of RNA Messenger RNA (mrna) Transfer RNA (trna) Ribosomal RNA (rrna) Functions Carries information specifying amino acid sequences of proteins from DNA to ribosomes Serves as adapter molecule in protein synthesis; translates mrna codons into amino acids Plays catalytic (ribozyme) roles and structural roles in ribosomes Type of RNA Primary transcript Small nuclear RNA (snrna) SRP RNA Functions Serves as a precursor to mrna, rrna, or trna, before being processed by splicing or cleavage Plays structural and catalytic roles in spliceosomes Is a component of the the signalrecognition particle (SRP)

31 Type of RNA Small nucleolar RNA (snorna) Small interfering RNA (sirna) and microrna (mirna) Functions Aids in processing pre-rrna transcripts for ribosome subunit formation in the nucleolus Are involved in regulation of gene expression RNA s diverse functions range from structural to informational to catalytic Properties that enable RNA to perform many different functions: Can hydrogen-bond to other nucleic acids Can assume a three-dimensional shape Has functional groups that allow it to act as a catalyst (ribozyme)

32 While gene expression differs among the domains of life, the concept of a gene is universal Archaea are prokaryotes, but share many features of gene expression with eukaryotes Comparing Gene Expression in Bacteria, Archaea, and Eukarya Bacteria and eukarya differ in their RNA polymerases, termination of transcription and ribosomes; archaea tend to resemble eukarya in these respects Bacteria can simultaneously transcribe and translate the same gene In eukarya, transcription and translation are separated by the nuclear envelope. In addition extensive RNA processing occurs in the nucleus In archaea, transcription and translation are likely coupled

33 RNA polymerase RNA polymerase Polyribosome Polypeptide (amino end) DNA Polyribosome Direction of transcription Ribosome mrna ( end) mrna 0.25 µm DNA Coupled transcription and translation in bacteria. In bacterial cells, the translation of mrna can begin as soon as the leading (5 ) end of the mrna molecule peels away from the DNA template. The micrograph (TEM) shows a strand of E coli DNA being transcribed by RNA polymerase molecules. Attached to each RNA polymerase molecule is a growing strand of mrna which is already being translated by ribosomes. The newly synthesized polypeptides are not visible in the micrograph but are shown in the diagram. What Is a Gene? Revisiting the Question The idea of the gene itself is a unifying concept of life We have considered a gene as: A discrete unit of inheritance A region of specific nucleotide sequence in a chromosome A DNA sequence that codes for a specific polypeptide chain In summary, a gene can be defined as a region of DNA that can be expressed to produce a final functional product, either a polypeptide or an RNA molecule

34 A summary of transcription and translation in a eukaryotic cell 1) Transcription- RNA is transcribed from a DNA template. 2) RNA processing- In eukaryotes the RNA transcript (pre mrna) is spliced and modified to produce mrna, which moves from the nucleus to the cytoplasm 3) The mrna leaves the nucleus and attaches to a ribosome 4) Amino acid activation- Each amino acid attaches to its proper trna with the help of a specific enzyme and ATP. 5) Translation- A succession of trnas add their amino acids to the polypeptide chain as the mrna is moved through the ribosome one codon at a time (When completed the polypeptide is released from the ribosome Conducting the Genetic Orchestra Prokaryotes and eukaryotes alter gene expression in response to their changing environment In multicellular eukaryotes, gene expression regulates development and is responsible for differences in cell types RNA molecules play many roles in regulating gene expression in eukaryotes

35 Individual bacteria respond to environmental change by regulating their gene expression A bacterium can tune its metabolism to the changing environment and food sources This metabolic control occurs on two levels: Adjusting activity of metabolic enzymes Regulating genes that encode metabolic enzymes Bacteria often respond to environmental change by regulating transcription Natural selection has favored bacteria that produce only the products needed by that cell A cell can regulate the production of enzymes by feedback inhibition or by gene regulation Gene expression in bacteria is controlled by the operon model

36 Operons: The Basic Concept An operon is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control In bacteria, genes are often clustered into operons, composed of An operator, an on-off switch A promoter Genes for metabolic enzymes A cluster of functionally related genes can be under coordinated control by a single on-off switch The regulatory switch is a segment of DNA called an operator usually positioned within the promoter The operon can be switched off by a protein repressor The repressor prevents gene transcription by binding to the operator and blocking RNA polymerase The repressor is the product of a separate regulatory gene The repressor can be in an active or inactive form, depending on the presence of other molecules A corepressor is a molecule that cooperates with a repressor protein to switch an operon off

37 Eukaryotic gene expression can be regulated at any stage All organisms must regulate which genes are expressed at any given time In multicellular organisms gene expression is essential for cell specialization Differential Gene Expression Almost all the cells in an organism are genetically identical Differences between cell types result from differential gene expression, the expression of different genes by cells with the same genome In each type of differentiated cell, a unique subset of genes is expressed Many key stages of gene expression can be regulated in eukaryotic cells Errors in gene expression can lead to diseases including cancer Gene expression is regulated at many stages

38 All our cells start off with the same set of genes A small percentage of these genes are expressed in all our cells- housekeeping genes like for example for glycolysis Through development and our lives different cells selectively express different genes For example RBCs transcribe hemoglobin genes whereas the eye does not transcribe this gene and instead it expresses crystalline Signal DNA RNA Cap Gene NUCLEUS Chromatin Chromatin modification DNA unpacking involving histone acetylation and DNA demethylation Exon Intron Tail Gene available for transcription Transcription Primary transcript RNA processing mrna in nucleus Transport to cytoplasm CYTOPLASM Stages in gene expression that can be regulated in eukaryotic cells. In this diagram the colored boxes indicate the processes most often regulated; each color indicates the type pf molecule that is affected (blue=dna, orange= RNA, purple= protein). The nuclear envelope separating transcription from translation in eukaryotic cells offers an opportunity for post transcriptional control in the form of RNA processing that is absent in prokaryotes. In addition eukaryotes have a greater variety of control mechanisms operating before transcription and after translation. The expression of any given gene, however does not necessarily involve every stage shown; for example not every polypeptide is cleaved.

39 CYTOPLASM mrna in cytoplasm Degradation of mrna Translation Polypeptide Protein processing such as cleavage and chemical modification Degradation of protein Active protein Transport to cellular destination Cellular function (such as enzymatic activity, structural support etc.) Controls before transcription Promoters Enhancers Methylation and acetylation Rearrangement- multiplication- for example polytene chromosomes contain several copies of genes allowing more RNA and subsequently more proteins to get produced

40 Regulation of Chromatin Structure Genes within highly packed heterochromatin are usually not expressed Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression Histone Modifications In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails This process loosens chromatin structure, thereby promoting the initiation of transcription The addition of methyl groups (methylation) can condense chromatin; the addition of phosphate groups (phosphorylation) next to a methylated amino acid can loosen chromatin The histone code hypothesis proposes that specific combinations of modifications help determine chromatin configuration and influence transcription

41 Histone tails DNA double helix Amino acids available for chemical modification (a) Histone tails protrude outward from a nucleosome. This is an end view of a nucleosome. The amino acids in the Ntermincal tails are accessible for chemical modification Unacetylated histones Acetylated histones A simple model of histone tails and the effect of histone acetylation. In addition to acetylation histones can undergo several other types of modifications that also help determine the chromatin configuration in a region. (b) Acetylation of histone tails promotes loose chromatin structure that permits transcription. A region of chromatin in which nucleosomes are unacetylated forms a compact structure (left) in which the DNA is not transcribed. When nucleosomes are highly acetylated (right) the chromatin becomes less compact, and the DNA is accessible for transcription DNA Methylation DNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species DNA methylation can cause long-term inactivation of genes in cellular differentiation In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development

42 Chemical Modifications Methylation of DNA can inactivate genes Acetylation of histones allows DNA unpacking and transcription Methylation of histone or of DNA usually turns a gene off. Acetylation of histone usually turns a gene on.

43 Epigenetic Inheritance Although the chromatin modifications just discussed do not alter DNA sequence, they may be passed to future generations of cells The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance Regulation of Transcription Initiation Chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery

44 Organization of a Typical Eukaryotic Gene Associated with most eukaryotic genes are control elements, segments of noncoding DNA that help regulate transcription by binding certain proteins Control elements and the proteins they bind are critical to the precise regulation of gene expression in different cell types Enhancer (distal control elements) DNA Upstream Proximal control elements Primary RNA Transcript (pre-mrna) mrna Promoter Intron RNA Cap Exon Intron Exon Exon Intron Exon Intron Exon 5 UTR untranslated region Coding segment Start codon Poly-A signal sequence Termination region Intron Exon Transcription RNA processing Cap and tail added introns excised and exons spliced together Downstream Cleaved end of primary transcript Poly-A signal Stop codon UTR Poly-A tail A eukaryotic gene and its transcript. Each eukaryotic gene has a promoter a DNA sequence where RNA polymerase binds and starts transcription proceeding downstream. A number of control elements (gold) are involved in regulating the initiation of transcription; these are DNA sequences located near (proximal to) or far from (distal to) the promoter. Distal control elements can be grouped together as enhancers one of which is shown for this gene. A polyadenylation (poly-a) signal sequence in the last exon of the gene is transcribed into an RNA sequence that signals where the transcript is cleaved and the poly A tail added. Transcription may continue for hundreds of nucleotides beyond the poly A signal before terminating. RNA processing of the primary transcript into a functional mrna involves three steps: addition of the 5 cap addition of the poly A tail and splicing. In the cell the 5 cap is added soon after transcription is initiated splicing and poly A tail addition may also occur while transcription is till under way.

45 The Roles of Transcription Factors To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called transcription factors General transcription factors are essential for the transcription of all protein-coding genes In eukaryotes, high levels of transcription of particular genes depend on control elements interacting with specific transcription factors Enhancers and Specific Transcription Factors Proximal control elements are located close to the promoter Distal control elements, groups of which are called enhancers, may be far away from a gene or even located in an intron An activator is a protein that binds to an enhancer and stimulates transcription of a gene Bound activators cause mediator proteins to interact with proteins at the promoter

46 DNA Enhancer Activators 1) Activator proteins bind to distal control elements grouped as an enhancer in the DNA. This enhancer has three binding sites. 2) A DNA bending protein brings the bound activators closer to the promoter. General transcription factors mediator proteins and RNA polymerase are nearby. 3) The activators bind to certain mediator proteins and general transcription factors, helping them form an active transcription initiation complex on the promoter. Distal control element DNA-bending protein Promoter TATA box General transcription factors Gene Group of mediator proteins A model for the action of enhancers and transcription activators: Bending of the DNA by a proteins enables enhancers the influence a promoter hundreds or even thousands of nucleotides away. Specific transcription factors called activators bind to the enhancer DNA sequences and then to a group of mediator proteins, which in turn bind to general transcription factors assembling the transcription initiation complex. These protein protein interactions facilitate the correct positioning of the complex on the promoter and the initiation of RNA synthesis. Only one enhancer (with three orange control elements) is shown here, but a gene may have several enhancers that act at different times or on different cell types Transcription initiation complex RNA polymerase II RNA polymerase II RNA synthesis Coordinately Controlled Genes in Eukaryotes Unlike the genes of a prokaryotic operon, each of the coordinately controlled eukaryotic genes has a promoter and control elements These genes can be scattered over different chromosomes, but each has the same combination of control elements Copies of the activators recognize specific control elements and promote simultaneous transcription of the genes

47 Mechanisms of Post-Transcriptional Regulation Transcription alone does not account for gene expression Regulatory mechanisms can operate at various stages after transcription Such mechanisms allow a cell to fine-tune gene expression rapidly in response to environmental changes Control of RNA processing In alternative RNA splicing, different mrna molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns Alternative splicing- For example different muscle cells express slightly different forms of the troponin gene by utilizing alternative splicing. This generates proteins with somewhat unique functions Nuclear envelope- UTRs contain zipcodes which allow the RNA to exit the nucleus with the aid of proteins which recognize it and selectively bind to it. In addition these unique zipcodes specify to which cytoplasmic location these RNA must move. This is crucial during embryonic development.

48 Exons DNA Troponin T gene Primary RNA transcript mrna RNA splicing Alternative RNA splicing of the troponin T gene. The primary transcript of this gene can be spliced in more than one way, generating different mrna molecules. Notice that one mrna molecule has ended up with exon 3 (green) and the other with exon 4 (purple). These two mrnas are translated into different but related muscle proteins. or mrna Degradation The life span of mrna molecules in the cytoplasm is a key to determining protein synthesis Eukaryotic mrna is more long lived than prokaryotic mrna The mrna life span is determined in part by sequences in the leader and trailer regions

49 Initiation of Translation The initiation of translation of selected mrnas can be blocked by regulatory proteins that bind to sequences or structures of the mrna Alternatively, translation of all mrnas in a cell may be regulated simultaneously For example, translation initiation factors are simultaneously activated in an egg following fertilization Protein Processing and Degradation After translation, various types of protein processing, including cleavage and the addition of chemical groups, are subject to control Proteasomes are giant protein complexes that bind protein molecules and degrade them

50 1) Multiple ubiquitin molecules are attached to a protein by enzymes in the cytosol Ubiquitin 2) The ubiquitin tagged protein is recognized by a proteasome which unfolds the protein and sequesters it within a central cavity Proteasome 3) Enzymatic components of the proteasome cut the protein into small peptides which can be further degraded by other enzymes in the cytosol. Proteasome and ubiquitin to be recycled Protein to be degraded Ubiquitinated protein Protein entering a proteasome Protein fragments (peptides) Degradation of a protein by a proteasome. A proteasome, an enormous protein complex shaped like a trash can, chops up unneeded proteins in the cell. In most cases the proteins attacked by a proteasome have been tagged with short chains of ubquitin a small protein. Steps 1 and 3 require ATP. Eukaryotic proteasomes are as massive as ribosomal subunits and are distributed throughout the cell. Their shape somewhat resembles that of chaperone proteins, which protect protein structure rather than destroy it Control after translation (post-translational) Example: phosphorylation and other protein modifications which occur after the protein has been synthesized can change their activity

51 Noncoding RNAs play multiple roles in controlling gene expression Only a small fraction of DNA codes for proteins, rrna, and trna A significant amount of the genome may be transcribed into noncoding RNAs Noncoding RNAs regulate gene expression at two points: mrna translation and chromatin configuration Effects on mrnas by MicroRNAs and Small Interfering RNAs MicroRNAs (mirnas) are small single-stranded RNA molecules that can bind to mrna These can degrade mrna or block its translation

52 (a) (b) Primary mirna transcript. This RNA molecule is transcribed from a gene in a nematode worm. Each double stranded region that ends in a loop is called a hairpin and generates one mirna (shown in orange) Regulation of gene expression by mirnas. RNA transcripts are processed into mirnas which prevent expression of mrnas containing complementary sequences. Hairpin mirna mirna Hydrogen bond Dicer 1) An enzyme cuts each hairpin from the primary mirna transcript 2) A second enzyme called Dicer, trims the loop and the single stranded ends from the hairpin, cutting at the arrows. 3) One strand of the double stranded RNA is degraded; the other strand (mirna) then forms mirnaprotein a complex with one complex or more proteins 4) The mirna in the complex can bind to any target mrna that contains at least 6 bases of complementary sequence. 5) If mirna and mrna are complementary all along their length, the mrna is mrna degraded Translation blocked degraded (left); if the match is less (b) Generation and function of mirnas complete translation is blocked (right) The phenomenon of inhibition of gene expression by RNA molecules is called RNA interference (RNAi). This is caused by single-stranded small interfering RNAs (sirnas) and can lead to degradation of an mrna or block its translation sirnas and mirnas are similar but form from different RNA precursors

53 Chromatin Remodeling and Silencing of Transcription by Small RNAs sirnas play a role in heterochromatin formation and can block large regions of the chromosome Small RNAs may also block transcription of specific genes

Lecture Series 7. From DNA to Protein. Genotype to Phenotype. Reading Assignments. A. Genes and the Synthesis of Polypeptides

Lecture Series 7. From DNA to Protein. Genotype to Phenotype. Reading Assignments. A. Genes and the Synthesis of Polypeptides Lecture Series 7 From DNA to Protein: Genotype to Phenotype Reading Assignments Read Chapter 7 From DNA to Protein A. Genes and the Synthesis of Polypeptides Genes are made up of DNA and are expressed

More information

Protein Synthesis How Genes Become Constituent Molecules

Protein Synthesis How Genes Become Constituent Molecules Protein Synthesis Protein Synthesis How Genes Become Constituent Molecules Mendel and The Idea of Gene What is a Chromosome? A chromosome is a molecule of DNA 50% 50% 1. True 2. False True False Protein

More information

Genetic information (DNA) determines structure of proteins DNA RNA proteins cell structure 3.11 3.15 enzymes control cell chemistry ( metabolism )

Genetic information (DNA) determines structure of proteins DNA RNA proteins cell structure 3.11 3.15 enzymes control cell chemistry ( metabolism ) Biology 1406 Exam 3 Notes Structure of DNA Ch. 10 Genetic information (DNA) determines structure of proteins DNA RNA proteins cell structure 3.11 3.15 enzymes control cell chemistry ( metabolism ) Proteins

More information

Transcription and Translation of DNA

Transcription and Translation of DNA Transcription and Translation of DNA Genotype our genetic constitution ( makeup) is determined (controlled) by the sequence of bases in its genes Phenotype determined by the proteins synthesised when genes

More information

RNA & Protein Synthesis

RNA & Protein Synthesis RNA & Protein Synthesis Genes send messages to cellular machinery RNA Plays a major role in process Process has three phases (Genetic) Transcription (Genetic) Translation Protein Synthesis RNA Synthesis

More information

a. Ribosomal RNA rrna a type ofrna that combines with proteins to form Ribosomes on which polypeptide chains of proteins are assembled

a. Ribosomal RNA rrna a type ofrna that combines with proteins to form Ribosomes on which polypeptide chains of proteins are assembled Biology 101 Chapter 14 Name: Fill-in-the-Blanks Which base follows the next in a strand of DNA is referred to. as the base (1) Sequence. The region of DNA that calls for the assembly of specific amino

More information

From DNA to Protein. Proteins. Chapter 13. Prokaryotes and Eukaryotes. The Path From Genes to Proteins. All proteins consist of polypeptide chains

From DNA to Protein. Proteins. Chapter 13. Prokaryotes and Eukaryotes. The Path From Genes to Proteins. All proteins consist of polypeptide chains Proteins From DNA to Protein Chapter 13 All proteins consist of polypeptide chains A linear sequence of amino acids Each chain corresponds to the nucleotide base sequence of a gene The Path From Genes

More information

BCH401G Lecture 39 Andres

BCH401G Lecture 39 Andres BCH401G Lecture 39 Andres Lecture Summary: Ribosome: Understand its role in translation and differences between translation in prokaryotes and eukaryotes. Translation: Understand the chemistry of this

More information

Translation. Translation: Assembly of polypeptides on a ribosome

Translation. Translation: Assembly of polypeptides on a ribosome Translation Translation: Assembly of polypeptides on a ribosome Living cells devote more energy to the synthesis of proteins than to any other aspect of metabolism. About a third of the dry mass of a cell

More information

Name Date Period. 2. When a molecule of double-stranded DNA undergoes replication, it results in

Name Date Period. 2. When a molecule of double-stranded DNA undergoes replication, it results in DNA, RNA, Protein Synthesis Keystone 1. During the process shown above, the two strands of one DNA molecule are unwound. Then, DNA polymerases add complementary nucleotides to each strand which results

More information

Lecture 4. Polypeptide Synthesis Overview

Lecture 4. Polypeptide Synthesis Overview Initiation of Protein Synthesis (4.1) Lecture 4 Polypeptide Synthesis Overview Polypeptide synthesis proceeds sequentially from N Terminus to C terminus. Amino acids are not pre-positioned on a template.

More information

AP BIOLOGY 2009 SCORING GUIDELINES

AP BIOLOGY 2009 SCORING GUIDELINES AP BIOLOGY 2009 SCORING GUIDELINES Question 4 The flow of genetic information from DNA to protein in eukaryotic cells is called the central dogma of biology. (a) Explain the role of each of the following

More information

Coding sequence the sequence of nucleotide bases on the DNA that are transcribed into RNA which are in turn translated into protein

Coding sequence the sequence of nucleotide bases on the DNA that are transcribed into RNA which are in turn translated into protein Assignment 3 Michele Owens Vocabulary Gene: A sequence of DNA that instructs a cell to produce a particular protein Promoter a control sequence near the start of a gene Coding sequence the sequence of

More information

Specific problems. The genetic code. The genetic code. Adaptor molecules match amino acids to mrna codons

Specific problems. The genetic code. The genetic code. Adaptor molecules match amino acids to mrna codons Tutorial II Gene expression: mrna translation and protein synthesis Piergiorgio Percipalle, PhD Program Control of gene transcription and RNA processing mrna translation and protein synthesis KAROLINSKA

More information

Chem 465 Biochemistry II

Chem 465 Biochemistry II Chem 465 Biochemistry II Name: 2 points Multiple choice (4 points apiece): 1. Formation of the ribosomal initiation complex for bacterial protein synthesis does not require: A) EF-Tu. B) formylmethionyl

More information

CHAPTER 40 The Mechanism of Protein Synthesis

CHAPTER 40 The Mechanism of Protein Synthesis CHAPTER 40 The Mechanism of Protein Synthesis Problems: 2,3,6,7,9,13,14,15,18,19,20 Initiation: Locating the start codon. Elongation: Reading the codons (5 3 ) and synthesizing protein amino carboxyl.

More information

The world of non-coding RNA. Espen Enerly

The world of non-coding RNA. Espen Enerly The world of non-coding RNA Espen Enerly ncrna in general Different groups Small RNAs Outline mirnas and sirnas Speculations Common for all ncrna Per def.: never translated Not spurious transcripts Always/often

More information

DNA (genetic information in genes) RNA (copies of genes) proteins (functional molecules) directionality along the backbone 5 (phosphate) to 3 (OH)

DNA (genetic information in genes) RNA (copies of genes) proteins (functional molecules) directionality along the backbone 5 (phosphate) to 3 (OH) DNA, RNA, replication, translation, and transcription Overview Recall the central dogma of biology: DNA (genetic information in genes) RNA (copies of genes) proteins (functional molecules) DNA structure

More information

The Steps. 1. Transcription. 2. Transferal. 3. Translation

The Steps. 1. Transcription. 2. Transferal. 3. Translation Protein Synthesis Protein synthesis is simply the "making of proteins." Although the term itself is easy to understand, the multiple steps that a cell in a plant or animal must go through are not. In order

More information

The sequence of bases on the mrna is a code that determines the sequence of amino acids in the polypeptide being synthesized:

The sequence of bases on the mrna is a code that determines the sequence of amino acids in the polypeptide being synthesized: Module 3F Protein Synthesis So far in this unit, we have examined: How genes are transmitted from one generation to the next Where genes are located What genes are made of How genes are replicated How

More information

PRACTICE TEST QUESTIONS

PRACTICE TEST QUESTIONS PART A: MULTIPLE CHOICE QUESTIONS PRACTICE TEST QUESTIONS DNA & PROTEIN SYNTHESIS B 1. One of the functions of DNA is to A. secrete vacuoles. B. make copies of itself. C. join amino acids to each other.

More information

Announcements. Chapter 15. Proteins: Function. Proteins: Function. Proteins: Structure. Peptide Bonds. Lab Next Week. Help Session: Monday 6pm LSS 277

Announcements. Chapter 15. Proteins: Function. Proteins: Function. Proteins: Structure. Peptide Bonds. Lab Next Week. Help Session: Monday 6pm LSS 277 Lab Next Week Announcements Help Session: Monday 6pm LSS 277 Office Hours Chapter 15 and Translation Proteins: Function Proteins: Function Enzymes Transport Structural Components Regulation Communication

More information

DNA, RNA, Protein synthesis, and Mutations. Chapters 12-13.3

DNA, RNA, Protein synthesis, and Mutations. Chapters 12-13.3 DNA, RNA, Protein synthesis, and Mutations Chapters 12-13.3 1A)Identify the components of DNA and explain its role in heredity. DNA s Role in heredity: Contains the genetic information of a cell that can

More information

Protein Synthesis. Page 41 Page 44 Page 47 Page 42 Page 45 Page 48 Page 43 Page 46 Page 49. Page 41. DNA RNA Protein. Vocabulary

Protein Synthesis. Page 41 Page 44 Page 47 Page 42 Page 45 Page 48 Page 43 Page 46 Page 49. Page 41. DNA RNA Protein. Vocabulary Protein Synthesis Vocabulary Transcription Translation Translocation Chromosomal mutation Deoxyribonucleic acid Frame shift mutation Gene expression Mutation Point mutation Page 41 Page 41 Page 44 Page

More information

TRANSCRIPTION TRANSLATION - GENETIC CODE AND OUTLINE OF PROTEIN SYNTHESIS

TRANSCRIPTION TRANSLATION - GENETIC CODE AND OUTLINE OF PROTEIN SYNTHESIS TRANSCRIPTION TRANSLATION - GENETIC CODE AND OUTLINE OF PROTEIN SYNTHESIS Central Dogma of Protein Synthesis Proteins constitute the major part by dry weight of an actively growing cell. They are widely

More information

RNA and Protein Synthesis

RNA and Protein Synthesis Name lass Date RN and Protein Synthesis Information and Heredity Q: How does information fl ow from DN to RN to direct the synthesis of proteins? 13.1 What is RN? WHT I KNOW SMPLE NSWER: RN is a nucleic

More information

CHAPTER 30: PROTEIN SYNTHESIS

CHAPTER 30: PROTEIN SYNTHESIS CHAPTER 30: PROTEIN SYNTHESIS (Translation) Translation: mrna protein LECTURE TOPICS Complexity, stages, rate, accuracy Amino acid activation [trna charging] trnas and translating the Genetic Code - Amino

More information

Provincial Exam Questions. 9. Give one role of each of the following nucleic acids in the production of an enzyme.

Provincial Exam Questions. 9. Give one role of each of the following nucleic acids in the production of an enzyme. Provincial Exam Questions Unit: Cell Biology: Protein Synthesis (B7 & B8) 2010 Jan 3. Describe the process of translation. (4 marks) 2009 Sample 8. What is the role of ribosomes in protein synthesis? A.

More information

To be able to describe polypeptide synthesis including transcription and splicing

To be able to describe polypeptide synthesis including transcription and splicing Thursday 8th March COPY LO: To be able to describe polypeptide synthesis including transcription and splicing Starter Explain the difference between transcription and translation BATS Describe and explain

More information

Chapter 5: Organization and Expression of Immunoglobulin Genes

Chapter 5: Organization and Expression of Immunoglobulin Genes Chapter 5: Organization and Expression of Immunoglobulin Genes I. Genetic Model Compatible with Ig Structure A. Two models for Ab structure diversity 1. Germ-line theory: maintained that the genome contributed

More information

Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources

Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources 1 of 8 11/7/2004 11:00 AM National Center for Biotechnology Information About NCBI NCBI at a Glance A Science Primer Human Genome Resources Model Organisms Guide Outreach and Education Databases and Tools

More information

2007 7.013 Problem Set 1 KEY

2007 7.013 Problem Set 1 KEY 2007 7.013 Problem Set 1 KEY Due before 5 PM on FRIDAY, February 16, 2007. Turn answers in to the box outside of 68-120. PLEASE WRITE YOUR ANSWERS ON THIS PRINTOUT. 1. Where in a eukaryotic cell do you

More information

mrna EDITING Watson et al., BIOLOGIA MOLECOLARE DEL GENE, Zanichelli editore S.p.A. Copyright 2005

mrna EDITING Watson et al., BIOLOGIA MOLECOLARE DEL GENE, Zanichelli editore S.p.A. Copyright 2005 mrna EDITING mrna EDITING http://dbb.urmc.rochester.edu/labs/smith/research_2.htm The number of A to I sites in the human transcriptome >15;000 the vast majority of these sites occurring in Alu repeats

More information

2013 W. H. Freeman and Company. 26 RNA Metabolism

2013 W. H. Freeman and Company. 26 RNA Metabolism 2013 W. H. Freeman and Company 26 RNA Metabolism CHAPTER 26 RNA Metabolism Key topics: Transcription: DNA-dependent synthesis of RNA Capping and splicing: RNA processing Overview of RNA Function Ribonucleic

More information

Micro RNAs: potentielle Biomarker für das. Blutspenderscreening

Micro RNAs: potentielle Biomarker für das. Blutspenderscreening Micro RNAs: potentielle Biomarker für das Blutspenderscreening micrornas - Background Types of RNA -Coding: messenger RNA (mrna) -Non-coding (examples): Ribosomal RNA (rrna) Transfer RNA (trna) Small nuclear

More information

Outline. interfering RNA - What is dat? Brief history of RNA interference. What does it do? How does it work?

Outline. interfering RNA - What is dat? Brief history of RNA interference. What does it do? How does it work? Outline Outline interfering RNA - What is dat? Brief history of RNA interference. What does it do? How does it work? What is RNA interference? Recently discovered regulatory level. Genome immune system.

More information

Sickle cell anemia: Altered beta chain Single AA change (#6 Glu to Val) Consequence: Protein polymerizes Change in RBC shape ---> phenotypes

Sickle cell anemia: Altered beta chain Single AA change (#6 Glu to Val) Consequence: Protein polymerizes Change in RBC shape ---> phenotypes Protein Structure Polypeptide: Protein: Therefore: Example: Single chain of amino acids 1 or more polypeptide chains All polypeptides are proteins Some proteins contain >1 polypeptide Hemoglobin (O 2 binding

More information

ISTEP+: Biology I End-of-Course Assessment Released Items and Scoring Notes

ISTEP+: Biology I End-of-Course Assessment Released Items and Scoring Notes ISTEP+: Biology I End-of-Course Assessment Released Items and Scoring Notes Page 1 of 22 Introduction Indiana students enrolled in Biology I participated in the ISTEP+: Biology I Graduation Examination

More information

Protein Synthesis CHAPTER OUTLINE

Protein Synthesis CHAPTER OUTLINE 40632_H08_151_188.qxp 12/14/06 12:12 PM Page 151 8 Protein Synthesis HAPTER UTLINE 8.1 8.2 8.3 8.4 8.5 8.6 8.7 Introduction Protein Synthesis ccurs by Initiation, Elongation, and Termination The ribosome

More information

BioBoot Camp Genetics

BioBoot Camp Genetics BioBoot Camp Genetics BIO.B.1.2.1 Describe how the process of DNA replication results in the transmission and/or conservation of genetic information DNA Replication is the process of DNA being copied before

More information

NO CALCULATORS OR CELL PHONES ALLOWED

NO CALCULATORS OR CELL PHONES ALLOWED Biol 205 Exam 1 TEST FORM A Spring 2008 NAME Fill out both sides of the Scantron Sheet. On Side 2 be sure to indicate that you have TEST FORM A The answers to Part I should be placed on the SCANTRON SHEET.

More information

CSC 2427: Algorithms for Molecular Biology Spring 2006. Lecture 16 March 10

CSC 2427: Algorithms for Molecular Biology Spring 2006. Lecture 16 March 10 CSC 2427: Algorithms for Molecular Biology Spring 2006 Lecture 16 March 10 Lecturer: Michael Brudno Scribe: Jim Huang 16.1 Overview of proteins Proteins are long chains of amino acids (AA) which are produced

More information

trna Processing and Modification

trna Processing and Modification trna Processing and Modification RNA POL III - TRANSCRIPTS 5S RNA, trna, repetitive Sequenzen (Alu-typ), versch. kleine stabile RNAs (7SL - RNA vom signal recognition particle (SRP)), U6 RNA 5S RNA nicht

More information

Gene Regulation -- The Lac Operon

Gene Regulation -- The Lac Operon Gene Regulation -- The Lac Operon Specific proteins are present in different tissues and some appear only at certain times during development. All cells of a higher organism have the full set of genes:

More information

MOLECULAR BIOLOGY. Translation. Kolluru. V. A. Ramaiah Professor Department of Biochemistry University of Hyderabad. (Revised 30-Oct-2007)

MOLECULAR BIOLOGY. Translation. Kolluru. V. A. Ramaiah Professor Department of Biochemistry University of Hyderabad. (Revised 30-Oct-2007) MOLECULAR BIOLOGY Translation Kolluru. V. A. Ramaiah Professor Department of Biochemistry University of Hyderabad (Revised 30-Oct-2007) CONTENTS Introduction Messenger RNA (mrna) Splicing Addition of 5

More information

Chapter 5. The Structure and Function of Macromolecule s

Chapter 5. The Structure and Function of Macromolecule s Chapter 5 The Structure and Function of Macromolecule s Most Macromolecules are polymers: Polymer: (poly: many; mer: part) Large molecules consisting of many identical or similar subunits connected together.

More information

Functional and Biomedical Aspects of Genome Research

Functional and Biomedical Aspects of Genome Research Functional and Biomedical Aspects of Genome Research 20 11 35 Vorlesung SS 04 Bartsch, Jockusch & Schmitt-John Mi. 9:15-10:00, in W7-135 13 Functional RNAs Thomas Schmitt-John micro RNAs small interfering

More information

Proteins. Proteins. Amino Acids. Most diverse and most important molecule in. Functions: Functions (cont d)

Proteins. Proteins. Amino Acids. Most diverse and most important molecule in. Functions: Functions (cont d) Proteins Proteins Most diverse and most important molecule in living i organisms Functions: 1. Structural (keratin in hair, collagen in ligaments) 2. Storage (casein in mother s milk) 3. Transport (HAEMOGLOBIN!)

More information

Biological Sciences Initiative. Human Genome

Biological Sciences Initiative. Human Genome Biological Sciences Initiative HHMI Human Genome Introduction In 2000, researchers from around the world published a draft sequence of the entire genome. 20 labs from 6 countries worked on the sequence.

More information

8. Peptide bonds, polypeptides and proteins

8. Peptide bonds, polypeptides and proteins 8. Peptide bonds, polypeptides and proteins In which we consider the nature of proteins, how they are synthesized, how they are assembled,, how they get to where they need to go within the cell and the

More information

Shu-Ping Lin, Ph.D. E-mail: splin@dragon.nchu.edu.tw

Shu-Ping Lin, Ph.D. E-mail: splin@dragon.nchu.edu.tw Amino Acids & Proteins Shu-Ping Lin, Ph.D. Institute te of Biomedical Engineering ing E-mail: splin@dragon.nchu.edu.tw Website: http://web.nchu.edu.tw/pweb/users/splin/ edu tw/pweb/users/splin/ Date: 10.13.2010

More information

What makes cells different from each other? How do cells respond to information from environment?

What makes cells different from each other? How do cells respond to information from environment? What makes cells different from each other? How do cells respond to information from environment? Regulation of: - Transcription - prokaryotes - eukaryotes - mrna splicing - mrna localisation and translation

More information

V22: involvement of micrornas in GRNs

V22: involvement of micrornas in GRNs What are micrornas? V22: involvement of micrornas in GRNs How can one identify micrornas? What is the function of micrornas? Elisa Izaurralde, MPI Tübingen Huntzinger, Izaurralde, Nat. Rev. Genet. 12,

More information

4. Which carbohydrate would you find as part of a molecule of RNA? a. Galactose b. Deoxyribose c. Ribose d. Glucose

4. Which carbohydrate would you find as part of a molecule of RNA? a. Galactose b. Deoxyribose c. Ribose d. Glucose 1. How is a polymer formed from multiple monomers? a. From the growth of the chain of carbon atoms b. By the removal of an OH group and a hydrogen atom c. By the addition of an OH group and a hydrogen

More information

Helices From Readily in Biological Structures

Helices From Readily in Biological Structures The α Helix and the β Sheet Are Common Folding Patterns Although the overall conformation each protein is unique, there are only two different folding patterns are present in all proteins, which are α

More information

Lecture Overview. Hydrogen Bonds. Special Properties of Water Molecules. Universal Solvent. ph Scale Illustrated. special properties of water

Lecture Overview. Hydrogen Bonds. Special Properties of Water Molecules. Universal Solvent. ph Scale Illustrated. special properties of water Lecture Overview special properties of water > water as a solvent > ph molecules of the cell > properties of carbon > carbohydrates > lipids > proteins > nucleic acids Hydrogen Bonds polarity of water

More information

A. A peptide with 12 amino acids has the following amino acid composition: 2 Met, 1 Tyr, 1 Trp, 2 Glu, 1 Lys, 1 Arg, 1 Thr, 1 Asn, 1 Ile, 1 Cys

A. A peptide with 12 amino acids has the following amino acid composition: 2 Met, 1 Tyr, 1 Trp, 2 Glu, 1 Lys, 1 Arg, 1 Thr, 1 Asn, 1 Ile, 1 Cys Questions- Proteins & Enzymes A. A peptide with 12 amino acids has the following amino acid composition: 2 Met, 1 Tyr, 1 Trp, 2 Glu, 1 Lys, 1 Arg, 1 Thr, 1 Asn, 1 Ile, 1 Cys Reaction of the intact peptide

More information

Concluding lesson. Student manual. What kind of protein are you? (Basic)

Concluding lesson. Student manual. What kind of protein are you? (Basic) Concluding lesson Student manual What kind of protein are you? (Basic) Part 1 The hereditary material of an organism is stored in a coded way on the DNA. This code consists of four different nucleotides:

More information

Appendix 2 Molecular Biology Core Curriculum. Websites and Other Resources

Appendix 2 Molecular Biology Core Curriculum. Websites and Other Resources Appendix 2 Molecular Biology Core Curriculum Websites and Other Resources Chapter 1 - The Molecular Basis of Cancer 1. Inside Cancer http://www.insidecancer.org/ From the Dolan DNA Learning Center Cold

More information

Built from 20 kinds of amino acids

Built from 20 kinds of amino acids Built from 20 kinds of amino acids Each Protein has a three dimensional structure. Majority of proteins are compact. Highly convoluted molecules. Proteins are folded polypeptides. There are four levels

More information

Protein Physics. A. V. Finkelstein & O. B. Ptitsyn LECTURE 1

Protein Physics. A. V. Finkelstein & O. B. Ptitsyn LECTURE 1 Protein Physics A. V. Finkelstein & O. B. Ptitsyn LECTURE 1 PROTEINS Functions in a Cell MOLECULAR MACHINES BUILDING BLOCKS of a CELL ARMS of a CELL ENZYMES - enzymatic catalysis of biochemical reactions

More information

Pipe Cleaner Proteins. Essential question: How does the structure of proteins relate to their function in the cell?

Pipe Cleaner Proteins. Essential question: How does the structure of proteins relate to their function in the cell? Pipe Cleaner Proteins GPS: SB1 Students will analyze the nature of the relationships between structures and functions in living cells. Essential question: How does the structure of proteins relate to their

More information

CHAPTER 3 THE CHEMISTRY OF ORGANIC MOLECULES

CHAPTER 3 THE CHEMISTRY OF ORGANIC MOLECULES CHAPTER 3 THE CHEMISTRY OF ORGANIC MOLECULES 3.1 Organic Molecules The chemistry of carbon accounts for the diversity of organic molecules found in living things. Carbon has six electrons, four of which

More information

Biosynthesis of Proteins

Biosynthesis of Proteins 718 FUNDAMENTALS F BICEMISTRY CNTENTS General Considerations Major Breakthroughs in Protein Synthesis Central Dogma of Molecular Genetics Phase of Protein Synthesis The Two Key Components in Protein Synthesis

More information

Review Packet- Modern Genetics

Review Packet- Modern Genetics Review Packet- Modern Genetics Name 1. Base your answer to the following question on The type of molecule represented below is found in organisms. 3. The diagram below represents a structure found in most

More information

Kaustubha Qanungo Ph.D Biological Sciences Trident Technical College 7000 Rivers Avenue Charleston SC 29464

Kaustubha Qanungo Ph.D Biological Sciences Trident Technical College 7000 Rivers Avenue Charleston SC 29464 Call for action: Paradigm shift in teaching microbiology in a community colleges Kaustubha Qanungo Ph.D Biological Sciences Trident Technical College 7000 Rivers Avenue Charleston SC 29464 Project Course:

More information

Human Genome and Human Genome Project. Louxin Zhang

Human Genome and Human Genome Project. Louxin Zhang Human Genome and Human Genome Project Louxin Zhang A Primer to Genomics Cells are the fundamental working units of every living systems. DNA is made of 4 nucleotide bases. The DNA sequence is the particular

More information

MOLECULAR BASIS OF INHERITANCE

MOLECULAR BASIS OF INHERITANCE CHAPTER 6 MOLECULAR BASIS OF INHERITANCE 6.1 The DNA 6.2 The Search for Genetic Material 6.3 RNA World 6.4 Replication 6.5 Transcription 6.6 Genetic Code 6.7 Translation 6.8 Regulation of Gene Expression

More information

AP BIOLOGY 2008 SCORING GUIDELINES

AP BIOLOGY 2008 SCORING GUIDELINES AP BIOLOGY 2008 SCORING GUIDELINES Question 1 1. The physical structure of a protein often reflects and affects its function. (a) Describe THREE types of chemical bonds/interactions found in proteins.

More information

RNAi Shooting the Messenger!

RNAi Shooting the Messenger! RNAi Shooting the Messenger! Bronya Keats, Ph.D. Department of Genetics Louisiana State University Health Sciences Center New Orleans Email: bkeats@lsuhsc.edu RNA interference (RNAi) A mechanism by which

More information

Insulin mrna to Protein Kit

Insulin mrna to Protein Kit Insulin mrna to Protein Kit A 3DMD Paper BioInformatics and Mini-Toober Folding Activity Teacher Key and Teacher Notes www. Insulin mrna to Protein Kit Contents Becoming Familiar with the Data... 3 Identifying

More information

mirnaselect pep-mir Cloning and Expression Vector

mirnaselect pep-mir Cloning and Expression Vector Product Data Sheet mirnaselect pep-mir Cloning and Expression Vector CATALOG NUMBER: MIR-EXP-C STORAGE: -80ºC QUANTITY: 2 vectors; each contains 100 µl of bacterial glycerol stock Components 1. mirnaselect

More information

Hormones: Classification. Hormones: Classification. Peptide Hormone Synthesis, Packaging, and Release

Hormones: Classification. Hormones: Classification. Peptide Hormone Synthesis, Packaging, and Release Hormones: Classification Hormones: Classification Be able to give types and example. Compare synthesis, half-life and location of receptor 1. Peptide or protein hormones Insulin from amino acids 2. Steroid

More information

srnas of Plants Small, Non-coding RNAs of Plants microrna ( mirnas small interfering RNA ( sirnas Plant mirnas MIR

srnas of Plants Small, Non-coding RNAs of Plants microrna ( mirnas small interfering RNA ( sirnas Plant mirnas MIR srnas of Plants Small, Non-coding RNAs of Plants Regulatory RNAs that act through gene silencing Two classes of small RNAs (srnas) o microrna (mirnas) Encoded by genes in the genome o small interfering

More information

REMOTE CONTROL by DNA as a Bio-sensor -antenna.

REMOTE CONTROL by DNA as a Bio-sensor -antenna. REMOTE CONTROL by DNA as a Bio-sensor -antenna. "Piezoelectric quantum transduction is a fundamental property of at- distance induction of genetic control " Paolo Manzelli: pmanzelli@gmail.com ; www.edscuola.it/lre.html;www.egocreanet.it

More information

Proteins and Nucleic Acids

Proteins and Nucleic Acids Proteins and Nucleic Acids Chapter 5 Macromolecules: Proteins Proteins Most structurally & functionally diverse group of biomolecules. : o Involved in almost everything o Enzymes o Structure (keratin,

More information

Lezioni Dipartimento di Oncologia Farmacologia Molecolare. RNA interference. Giovanna Damia 29 maggio 2006

Lezioni Dipartimento di Oncologia Farmacologia Molecolare. RNA interference. Giovanna Damia 29 maggio 2006 Lezioni Dipartimento di Oncologia Farmacologia Molecolare RNA interference Giovanna Damia 29 maggio 2006 RNA INTERFERENCE Sequence-specific gene suppression by dsrnas Gene silencing by dsrna: C. elegans

More information

8/20/2012 H C OH H R. Proteins

8/20/2012 H C OH H R. Proteins Proteins Rubisco monomer = amino acids 20 different amino acids polymer = polypeptide protein can be one or more polypeptide chains folded & bonded together large & complex 3-D shape hemoglobin Amino acids

More information

If and when cancer cells stop dividing, they do so at random points, not at the normal checkpoints in the cell cycle.

If and when cancer cells stop dividing, they do so at random points, not at the normal checkpoints in the cell cycle. Cancer cells have escaped from cell cycle controls Cancer cells divide excessively and invade other tissues because they are free of the body s control mechanisms. Cancer cells do not stop dividing when

More information

H H N - C - C 2 R. Three possible forms (not counting R group) depending on ph

H H N - C - C 2 R. Three possible forms (not counting R group) depending on ph Amino acids - 0 common amino acids there are others found naturally but much less frequently - Common structure for amino acid - C, -N, and functional groups all attached to the alpha carbon N - C - C

More information

DNA Fingerprinting. Unless they are identical twins, individuals have unique DNA

DNA Fingerprinting. Unless they are identical twins, individuals have unique DNA DNA Fingerprinting Unless they are identical twins, individuals have unique DNA DNA fingerprinting The name used for the unambiguous identifying technique that takes advantage of differences in DNA sequence

More information

Biology [SBI 4U] FINAL EXAMINATION

Biology [SBI 4U] FINAL EXAMINATION Biology [SBI 4U] FINAL EXAMINATION Date: November 28, 2012 (Wednesday) Time: 8:30 a.m. 10:30 a.m. Length: 2 hours Lecturer: Ms. Kimberley Gagnon Canadian International Matriculation Programme Student Name:

More information

Dicer Substrate RNAi Design

Dicer Substrate RNAi Design INTEGRATED DNA TECHNOLOGIES, INC. Dicer Substrate RNAi Design How to design and order 27-mer Dicer-substrate Duplex RNAs for use as RNA interference reagents The following document provides a summary of

More information

1. Molecular computation uses molecules to represent information and molecular processes to implement information processing.

1. Molecular computation uses molecules to represent information and molecular processes to implement information processing. Chapter IV Molecular Computation These lecture notes are exclusively for the use of students in Prof. MacLennan s Unconventional Computation course. c 2013, B. J. MacLennan, EECS, University of Tennessee,

More information

1. The diagram below represents a biological process

1. The diagram below represents a biological process 1. The diagram below represents a biological process 5. The chart below indicates the elements contained in four different molecules and the number of atoms of each element in those molecules. Which set

More information

School of Nursing. Presented by Yvette Conley, PhD

School of Nursing. Presented by Yvette Conley, PhD Presented by Yvette Conley, PhD What we will cover during this webcast: Briefly discuss the approaches introduced in the paper: Genome Sequencing Genome Wide Association Studies Epigenomics Gene Expression

More information

This class deals with the fundamental structural features of proteins, which one can understand from the structure of amino acids, and how they are

This class deals with the fundamental structural features of proteins, which one can understand from the structure of amino acids, and how they are This class deals with the fundamental structural features of proteins, which one can understand from the structure of amino acids, and how they are put together. 1 A more detailed view of a single protein

More information

http://faculty.sau.edu.sa/h.alshehri

http://faculty.sau.edu.sa/h.alshehri http://faculty.sau.edu.sa/h.alshehri Definition: Proteins are macromolecules with a backbone formed by polymerization of amino acids. Proteins carry out a number of functions in living organisms: - They

More information

The microscope is an important tool.

The microscope is an important tool. KEY CONCEPT Microscopes allow us to see inside the cell. BEFORE, you learned Some organisms are unicellular and some are multicellular A microscope is necessary to study most cells The cell theory describes

More information

How Cancer Begins???????? Chithra Manikandan Nov 2009

How Cancer Begins???????? Chithra Manikandan Nov 2009 Cancer Cancer is one of the most common diseases in the developed world: 1 in 4 deaths are due to cancer 1 in 17 deaths are due to lung cancer Lung cancer is the most common cancer in men Breast cancer

More information

v vi vii viii ix 1 2 for high school students. For this, research needed to be done to to find a popular and engaging style of animation for this age group. The third step was to design the animation so

More information

Chapter-21b: Hormones and Receptors

Chapter-21b: Hormones and Receptors 1 hapter-21b: Hormones and Receptors Hormone classes Hormones are classified according to the distance over which they act. 1. Autocrine hormones --- act on the same cell that released them. Interleukin-2

More information

18.2 Protein Structure and Function: An Overview

18.2 Protein Structure and Function: An Overview 18.2 Protein Structure and Function: An Overview Protein: A large biological molecule made of many amino acids linked together through peptide bonds. Alpha-amino acid: Compound with an amino group bonded

More information

IV. -Amino Acids: carboxyl and amino groups bonded to -Carbon. V. Polypeptides and Proteins

IV. -Amino Acids: carboxyl and amino groups bonded to -Carbon. V. Polypeptides and Proteins IV. -Amino Acids: carboxyl and amino groups bonded to -Carbon A. Acid/Base properties 1. carboxyl group is proton donor! weak acid 2. amino group is proton acceptor! weak base 3. At physiological ph: H

More information

Post-transcriptional control of gene expression

Post-transcriptional control of gene expression Post-transcriptional control of gene expression Possible post-transcriptional controls on gene expression Only a few of these controls are likely to be important for any one gene Mecanismo de processamento

More information

Hormones & Chemical Signaling

Hormones & Chemical Signaling Hormones & Chemical Signaling Part 2 modulation of signal pathways and hormone classification & function How are these pathways controlled? Receptors are proteins! Subject to Specificity of binding Competition

More information

PART 3.3: MicroRNA and Cancer

PART 3.3: MicroRNA and Cancer BIBM 2010 Tutorial: Epigenomics and Cancer PART 3.3: MicroRNA and Cancer Dec 18, 2010 Sun Kim at Indiana University Outline of Part 3.3 Background on microrna Role of microrna in cancer MicroRNA pathway

More information

Teacher Guide: Have Your DNA and Eat It Too ACTIVITY OVERVIEW. http://gslc.genetics.utah.edu

Teacher Guide: Have Your DNA and Eat It Too ACTIVITY OVERVIEW. http://gslc.genetics.utah.edu ACTIVITY OVERVIEW Abstract: Students build an edible model of DNA while learning basic DNA structure and the rules of base pairing. Module: The Basics and Beyond Prior Knowledge Needed: DNA contains heritable

More information

Guided Notes: Chapter 9 Cellular Reproduction

Guided Notes: Chapter 9 Cellular Reproduction Guided Notes: Cellular Reproduction When do cells divide? Cells grow and function normally until they become too. Cell size is because increases faster than This means that there is not enough area on

More information

Unit I: Introduction To Scientific Processes

Unit I: Introduction To Scientific Processes Unit I: Introduction To Scientific Processes This unit is an introduction to the scientific process. This unit consists of a laboratory exercise where students go through the QPOE2 process step by step

More information