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12.4 First Step: Transcription

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1 12.4 First Step: Transcription
A segment of DNA serves as a template for the production of an RNA molecule The gene unzips and exposes unpaired bases Serves as template for mRNA formation Loose RNA nucleotides bind to exposed DNA bases using the C=G and A=U rule When entire gene is transcribed into mRNA, the result is a pre-mRNA transcript of the gene The base sequence in the pre-mRNA is complementary to the base sequence in DNA

2 First Step: Transcription
A single chromosome consists of one very long molecule encoding hundreds or thousands of genes The genetic information in a gene describes the amino acid sequence of a protein The information is in the base sequence of one side (the “sense” strand) of the DNA molecule The gene is the functional equivalent of a “sentence” The segment of DNA corresponding to a gene is unzipped to expose the bases of the sense strand The genetic information in the gene is transcribed (rewritten) into an mRNA molecule The exposed bases in the DNA determine the sequence in which the RNA bases will be connected together RNA polymerase connects the loose RNA nucleotides together The completed transcript contains the information from the gene, but in a mirror image, or complementary form

3 Transcription 3′ 5′ terminator gene strand template strand T C G T 3′
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 3′ 5′ terminator gene strand template strand T C G T 3′ C G direction of polymerase movement A A T RNA polymerase T DNA template strand mRNA transcript promoter 5′ 5′ 3′ to RNA processing

4 © Oscar L. Miller/Photo Researchers, Inc.
RNA Polymerase Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. a. 200m spliceosome DNA RNA polymerase RNA transcripts © Oscar L. Miller/Photo Researchers, Inc. b.

5 First Step: Transcription
Pre-mRNA is modified before leaving the eukaryotic nucleus. Modifications to the ends of the primary transcript: Cap on the 5′ end The cap is a modified guanine (G) nucleotide Helps a ribosome determine where to attach when translation begins Poly-A tail of adenines on the 3′ end Facilitates the transport of mRNA out of the nucleus Inhibits degradation of mRNA by hydrolytic enzymes.

6 First Step: Transcription
Pre-mRNA, is composed of exons and introns. The exons will be expressed, The introns, occur in between the exons. Allows a cell to pick and choose which exons will go into a particular mRNA RNA splicing: Primary transcript consists of: Some segments that will not be expressed (introns) Segments that will be expressed (exons) Performed by spliceosome complexes in nucleoplasm Introns are excised Remaining exons are spliced back together Result is a mature mRNA transcript

7 First Step: Transcription
In prokaryotes, introns are removed by “self-splicing”—that is, the intron itself has the capability of enzymatically splicing itself out of a pre-mRNA

8 Messenger RNA Processing in Eukaryotes
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. DNA

9 Messenger RNA Processing in Eukaryotes
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. exon exon exon DNA intron intron 9

10 Messenger RNA Processing in Eukaryotes
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. exon exon exon DNA intron intron transcription exon exon exon pre-mRNA 5 intron intron 3 10

11 Messenger RNA Processing in Eukaryotes
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. exon exon exon DNA intron intron transcription exon exon exon pre-mRNA 5 intron intron 3 exon exon exon 3 5 cap 11 intron intron poly-A tail

12 Messenger RNA Processing in Eukaryotes
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. exon exon exon DNA intron intron transcription exon exon exon pre-mRNA 5 intron intron 3 exon exon exon 5 3 cap intron intron poly-A tail spliceosome exon exon exon 5 12 3 cap poly-A tail

13 Messenger RNA Processing in Eukaryotes
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. exon exon exon DNA intron intron transcription exon exon exon pre-mRNA 5 intron intron 3 exon exon exon 5 3 cap intron intron poly-A tail spliceosome exon exon exon 5 3 cap poly-A tail pre-mRNA splicing intron RNA mRNA 5 3 13 cap poly-A tail

14 Messenger RNA Processing in Eukaryotes
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. exon exon exon DNA intron intron transcription exon exon exon pre-mRNA 5 intron intron 3 exon exon exon 5 3 cap intron intron poly-A tail spliceosome exon exon exon 5 3 cap poly-A tail pre-mRNA splicing intron RNA mRNA 5 3 cap poly-A tail 14 cytoplasm

15 Messenger RNA Processing in Eukaryotes
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. exon exon exon DNA intron intron transcription exon exon exon pre-mRNA 5 intron intron 3 exon exon exon 5 3 cap intron intron poly-A tail spliceosome exon exon exon 5 3 cap poly-A tail pre-mRNA splicing intron RNA mRNA 5 3 cap poly-A tail nuclear pore in nuclear envelope nucleus 15 cytoplasm

16 First Step: Transcription
Functions of introns: As organismal complexity increases; The number of protein-coding genes does not keep pace But the proportion of the genome that is introns increases Possible functions of introns: Exons might combine in various combinations Would allow different mRNAs to result from one segment of DNA Introns might regulate gene expression Introns may encourage crossing-over during meiosis Exciting new picture of the genome is emerging

17 12.5 Second Step: Translation
The sequence of codons in the mRNA at a ribosome directs the sequence of amino acids into a polypeptide A nucleic acid sequence is translated into a protein sequence tRNA molecules have two binding sites: One associates with the mRNA transcript The other associates with a specific amino acid Each of the 20 amino acids in proteins associates with one or more of 64 types of tRNA An mRNA transcript associates with the rRNA of a ribosome in the cytoplasm or a ribosome associated with the rough endoplasmic reticulum The ribosome “reads” the information in the transcript Ribosome directs various types of tRNA to bring in their specific amino acid “fares” The tRNA specified is determined by the code being translated in the mRNA transcript

18 Second Step: Translation
tRNA molecules come in 64 different kinds All are very similar except that One end bears a specific triplet (of the 64 possible) called the anticodon The other end binds with a specific amino acid type tRNA synthetases attach the correct amino acid to the correct tRNA molecule All tRNA molecules with a specific anticodon will always bind with the same amino acid

19 Structure of a tRNA Molecule
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino acid leucine 3’ 5’ hydrogen bonding G A A

20 Structure of a tRNA Molecule
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino acid leucine 3’ 5’ hydrogen bonding amino acid end G A A 20

21 Structure of a tRNA Molecule
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino acid leucine 3’ 5’ hydrogen bonding amino acid end anticodon anticodon end G A A 21

22 Structure of a tRNA Molecule
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino acid leucine 3’ 5’ hydrogen bonding amino acid end anticodon anticodon end G A A C A G U C C U U C C U C mRNA 5’ 3’ 22

23 Structure of a tRNA Molecule
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino acid leucine 3’ 5’ hydrogen bonding amino acid end anticodon anticodon end G A A C A G U C C U U C C U C mRNA 5’ 3’ codon 23 a. b.

24 Second Step: Translation
Ribosomes Ribosomal RNA (rRNA): Produced from a DNA template in the nucleolus of a nucleus Combined with proteins into large and small ribosomal subunits A completed ribosome has three binding sites to facilitate pairing between tRNA and mRNA The E (for exit) site The P (for peptide) site, and The A (for amino acid) site

25 Ribosome Structure and Function
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. large subunit 5 3 A P E mRNA tRNA binding sites small subunit a. Structure of a ribosome b. Binding sites of ribosome outgoing tRNA polypeptide incoming tRNA mRNA c. Function of ribosomes d. Polyribosome Courtesy Alexander Rich

26 Second Step: Translation
Initiation: Components necessary for initiation are: Small ribosomal subunit mRNA transcript Initiator tRNA, and Large ribosomal subunit Initiation factors (special proteins that bring the above together) Initiator tRNA: Always has the UAC anticodon Always carries the amino acid methionine Capable of binding to the P site

27 Second Step: Translation
Small ribosomal subunit attaches to mRNA transcript Beginning of transcript always has the START codon (AUG) Initiator tRNA (UAC) attaches to P site Large ribosomal subunit joins the small subunit

28 Initiation amino acid methionine initiator tRNA U A 5 A C mRNA E site
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino acid methionine Met initiator tRNA U A 5 A C mRNA E site P site A site U G 3 Met small ribosomal subunit large ribosomal subunit U A C A U G 5 start codon 3 A small ribosomal subunit binds to mRNA; an initiator tRNA pairs with the mRNA start codon AUG. The large ribosomal subunit completes the ribosome. Initiator tRNA occupies the P site. The A site is ready for the next tRNA. Initiation

29 Second Step: Elongation
“Elongation” refers to the growth in length of the polypeptide RNA molecules bring their amino acid fares to the ribosome Ribosome reads a codon in the mRNA Allows only one type of tRNA to bring its amino acid Must have the anticodon complementary to the mRNA codon being read The incoming tRNA joins the ribosome at its A site Methionine of the initiator tRNA is connected to the amino acid of the 2nd tRNA by a peptide bond

30 Second Step: Elongation
The second tRNA moves to P site (translocation) The spent initiator tRNA moves to the E site and exits The ribosome reads the next codon in the mRNA Allows only one type of tRNA to bring its amino acid Must have the anticodon complementary to the mRNA codon being read Joins the ribosome at its A site The dipeptide on the 2nd amino acid is connected to the amino acid of the 3rd tRNA by a peptide bond

31 Elongation Met peptide bond Ser Ala Trp Val C A U G U A G A C 3 5
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Met peptide bond Ser Ala Trp Val C A U G U A G A C 3 5

32 Elongation A tRNA–amino acid approaches the ribosome and binds
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. asp Met peptide bond tRNA Ser C U G Ala Trp anticodon Val C A U G U A G A C 3 5 1 A tRNA–amino acid approaches the ribosome and binds at the A site. 32

33 Elongation A tRNA–amino acid approaches the ribosome and binds
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. asp Met Met peptide bond tRNA Ser Ser Ala C U G Ala Trp anticodon Trp Val Asp Val C A U C A U C U G G U A G A C G U A G A C 3 3 5 5 1 2 A tRNA–amino acid approaches the ribosome and binds at the A site. Two tRNAs can be at a ribosome at one time; the anticodons are paired to the codons. 33

34 Elongation 34 A tRNA–amino acid approaches the ribosome and binds
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Met asp Met Met Ser peptide bond tRNA Ser Ser Ala Ala C U G Ala Trp peptide bond Trp anticodon Trp Val Val Val Asp Asp C A U C A U C U G C A U C U G G U A G A C G U A G A C G U A G A C 3 5 3 5 5 3 1 A tRNA–amino acid approaches the ribosome and binds at the A site. 2 Two tRNAs can be at a ribosome at one time; the anticodons are paired to the codons. 3 Peptide bond formation attaches the peptide chain to the newly arrived amino acid. 34

35 Elongation 35 peptide bond tRNA peptide anticodon bond 1
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Met Met asp Met Met peptide bond tRNA Ser Ser Ser Ser Ala Ala Ala C U G Ala Trp peptide Trp Trp anticodon Trp Val bond Val Val Val Asp Asp Asp A U C C A U C A U C U G C A U C U G C U G G U A G A C G U A G A C G U A G A C G U A G A C A C C 3 5 3 5 5 3 5 3 1 A tRNA–amino acid approaches the ribosome and binds at the A site. 2 Two tRNAs can be at a ribosome at one time; the anticodons are paired to the codons. 3 Peptide bond formation attaches the peptide chain to the newly arrived amino acid. 4 The ribosome moves forward; the “empty” tRNA exits from the E site; the next amino acid–tRNA complex is approaching the ribosome. 35

36 Elongation 36 peptide bond tRNA peptide anticodon bond 1
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Met Met asp Met Met Thr peptide bond tRNA Ser Ser Ser Ser Ala Ala Ala C U G Ala Trp peptide Trp U G Trp anticodon Trp Val bond G Val Val Val Asp Asp Asp A U C C A U C A U C U G C A U C U G C U G G U A G A C G U A G A C G U A G A C G U A G A C A C C 3 3 5 5 5 3 5 3 1 A tRNA–amino acid approaches the ribosome and binds at the A site. 2 Two tRNAs can be at a ribosome at one time; the anticodons are paired to the codons. 3 Peptide bond formation attaches the peptide chain to the newly arrived amino acid. 4 The ribosome moves forward; the “empty” tRNA exits from the E site; the next amino acid–tRNA complex is approaching the ribosome. 36

37 Elongation 37 peptide bond tRNA peptide anticodon bond 1
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Met Met asp Met Met Ser Thr peptide bond tRNA Ser Ser Ser Ala Ala Ala C U G Ala Trp peptide Trp U G Trp anticodon Trp Val bond G Val Val Val Asp Asp Asp U C A C A U C A U C U G C A U C U G C U G G U A G A C G U A G A C G U A G A C G U A G A C A C C 3 5 3 5 5 3 5 3 1 A tRNA–amino acid approaches the ribosome and binds at the A site. 2 Two tRNAs can be at a ribosome at one time; the anticodons are paired to the codons. 3 Peptide bond formation attaches the peptide chain to the newly arrived amino acid. 4 The ribosome moves forward; the “empty” tRNA exits from the E site; the next amino acid–tRNA complex is approaching the ribosome. Elongation 37

38 Second Step: Translation
Termination: Previous tRNA moves to the P site Spent tRNA moves to the E site and exits Ribosome reads the STOP codon at the end of the mRNA UAA, UAG, or UGA Does not code for an amino acid A protein called a release factor binds to the stop codon and cleaves the polypeptide from the last tRNA The ribosome releases the mRNA and dissociates into subunits The same mRNA may be read by another ribosome

39 Termination release factor stop codon Termination 5′ 3′
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Asp Ala Trp release factor Asp Val Ala Glu Trp Val U U A A Glu U G A 5′ stop codon 3′ The ribosome comes to a stop codon on the mRNA. A release factor binds to the site. U C U A A U G G A 3′ 5′ The release factor hydrolyzes the bond between the last tRNA at the P site and the polypeptide, releasing them. The ribosomal subunits dissociate. Termination

40 Summary of Protein Synthesis in Eukaryotes
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. TRANSCRIPTION TRANSLATION 1. DNA in nucleus serves as a template for mRNA. DN A 3. mRNA moves into cytoplasm and becomes associated with ribosomes. 2. mRNA is processed before leaving the nucleus. large and small ribosomal subunits 5 mRNA introns pre-mRN A 3 mRN A amino acids 4. tRNAs with anticodons carry amino acids to mRNA. nuclear pore peptide ribosome tRNA U A C U A C 5 A U G 3 anticodon codon 5. During initiation, anticodon-codon complementary base pairing begins as the ribosomal subunits come together at a start codon. 8. During termination, a ribosome reaches a stop codon; mRNA and ribosomal subunits disband. C C C 5 C C C U G G U U U G G G A C C A A A G U A 3 6. During elongation, polypeptide synthesis takes place one amino acid at a time. 7. Ribosome attaches to rough ER. Polypeptide enters lumen, where it folds and is modified.

41 12.6 Structure of the Eukaryotic Chromosome
Each chromosome contains a single linear DNA molecule, but is composed of more than 50% protein. Some of these proteins are concerned with DNA and RNA synthesis Histones play primarily a structural role The most abundant proteins in chromosomes Five primary types of histone molecules Responsible for packaging the DNA The DNA double helix is wound at intervals around a core of eight histone molecules (called a nucleosome) Nucleosomes are joined by “linker” DNA.

42 Structure of Eukaryotic Chromosomes
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 2nm DNA double helix 11 nm 1. Wrapping of DNA around histone proteins. a. Nucleosomes (“beads on a string”) histones nucleosome histone H1 2. Formation of a three-dimensional zigzag structure via histone H1 and other DNA-binding proteins. b. 30-nm fiber 30 nm 300 nm 3. Loose coiling into radial loops . c. Radial loop domains euchromatin 4. Tight compaction of radial loops to form heterochromatin. 700 nm d. Heterochromatin 5. Metaphase chromosome forms with the help of a protein scaffold. 1,400 nm e. Metaphase chromosome a: © Ada L. Olins and Donald E. Olins/Biological Photo Service; b: Courtesy Dr. Jerome Rattner, Cell Biology and Anatomy, University of Calgary; c: Courtesy of Ulrich Laemmli and J.R. Paulson, Dept. of Molecular Biology, University of Geneva, Switzerland; d: © Peter Engelhardt/Department of Pathology and Virology, Haartman Institute/Centre of Excellence in Computational Complex Systems Research, Biomedical Engineering and Computational Science, Faculty of Information and Natural Sciences, Helsinki University of Technology, Helsinki, Finland

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