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Chapter 12

Chapter 12. Gene Expression and Regulation. How Is the Information in DNA Used in a Cell?. The link between DNA and protein DNA contains the “molecular blueprint” of every cell Proteins are the construction workers of the cell

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Chapter 12

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  1. Chapter 12 • Gene Expression and Regulation

  2. How Is the Information in DNA Used in a Cell? • The link between DNA and protein • DNA contains the “molecular blueprint” of every cell • Proteins are the construction workers of the cell • Proteins control cell shape, function, reproduction, and synthesis of biomolecules • Therefore, there must be a flow of information from DNA to protein

  3. How Is the Information in DNA Used in a Cell? • DNA provides instructions for protein synthesis via RNA intermediaries • DNA in eukaryotes is kept in the nucleus • Protein synthesis occurs at ribosomes in the cytoplasm • RNA differs structurally from DNA in three ways • RNA has the sugar ribose • RNA is usually single-stranded • RNA contains the nitrogenous base uracil (U) instead of thymine (T)

  4. How Is the Information in DNA Used in a Cell? • DNA provides instructions for protein synthesis via RNA intermediaries • There are three types of RNA involved in protein synthesis • Messenger RNA (mRNA) carries a copy of DNA gene information to the ribosome in the cytoplasm • Ribosomal RNA (rRNA) plus proteins make up the structure of ribosomes • Transfer RNA (tRNA) brings amino acids to the ribosome

  5. How Is the Information in DNA Used in a Cell? • DNA provides instructions for protein synthesis via RNA intermediaries • RNA occurs in many other roles besides protein synthesis • RNA is used as the genetic material in some viruses, such as HIV • Ribozymes – enzymatic RNA • “Regulatory” RNA • MicroRNA

  6. How Is the Information in DNA Used in a Cell? • Overview : Genetic information is transcribed into RNA and then translated into protein • mRNA carries the code for protein synthesis from DNA to the ribosomes • Ribosomal rRNA and proteins form ribosomes • Transfer tRNA carries amino acids to the ribosomes for addition to the growing protein

  7. How Is the Information in DNA Used in a Cell? • Overview: Genetic information is transcribed into RNA and then translated into protein • DNA directs protein synthesis in a two-step process • Transcription - Information in a DNA gene is copied into RNA (like a court transcription – same language just a copy of information) • Translation - the genetic information contained in the mRNA is converted to another language by Messenger RNA, tRNA, amino acids, and a ribosome, to synthesize a protein

  8. Genetic Information Flows from DNA to RNA to Protein gene DNA (nucleus) (cytoplasm) Transcription of the gene produces an mRNA with a nucleotide sequence complementary to one of the DNA strands (a) Transcription messenger RNA Translation of the mRNA produces a protein molecule with an amino acid sequence determined by the nucleotide sequence in the mRNA (b) Translation ribosome protein Fig. 12-2

  9. How Is the Information in DNA Used in a Cell? • The genetic code uses three bases to specify an amino acid • The genetic code provides the rules • Given that there are 20 amino acids but only four bases, statistically, the smallest number of bases that could combine to yield a different sequence for each of the 20 amino acids is three • A two-base code could produce only 16 combinations • The three-base code has the potential to create 64 combinations

  10. How Is the Information in DNA Used in a Cell? • The genetic code uses three bases to specify an amino acid • Marshall Nirenberg and Heinrich Matthaei cracked the genetic code by creating artificial mRNAs of known sequence and observing what proteins they produced • For example, an mRNA strand composed entirely of uracil (UUUUUUUU…) produced a protein consisting entirely of the amino acid phenylalanine • Therefore, they concluded that the triplet UUU is the codon for phenylalanine

  11. How Is the Information in DNA Used in a Cell? • The genetic code uses three bases to specify an amino acid • Base triplets in DNA(sequence of 3 nucleotides) • Codons in mRNA specifies a unique amino acid in the genetic code • Each mRNA also has a start codon (AUG) and one of three stop codons (UAG, UAA, and UGA) • Some amino acids are specified by as many as six different codons

  12. How Is the Information in DNA Used in a Cell? • The genetic code uses three bases to specify an amino acid • Decoding the codons of mRNA is the job of tRNA and ribosomes • Each unique tRNA has three exposed bases, called an anticodon, which are complementary to codon bases in mRNA

  13. How Is the Information in a Gene Transcribed into RNA? • Overview of transcription • Transcription of a DNA gene into RNA has three stages • Initiation - A promoter region at the beginning of the gene marks where transcription is to be initiated • Elongation - The “body” of the gene corresponds with where elongation of the RNA strand occurs • Termination - A termination signal at the end of the gene marks where RNA synthesis is to terminate

  14. Initiation DNA gene 3 gene 1 gene 2 RNA polymerase direction of transcription DNA promoter beginning of gene (3´ end) Initiation: RNA polymerase binds to the promoter region of DNA near the beginning of a gene, separating the double helix near the promoter. 1 Fig. 12-3 (1 of 4)

  15. Elongation RNA DNA template strand Elongation: RNA polymerase travels along the DNA template strand (blue), unwinding the DNA double helix and synthesizing RNA by catalyzing the addition of ribose nucleotides into an RNA molecule (red). The nucleotides in the RNA are complementary to the template strand of the DNA. 2 DNA  RNA C - G G - C T - A A - U Fig. 12-3 (2 of 4)

  16. Termination and Conclusion of Transcription Fig. 12-3 (3 & 4 of 4) termination signal Termination: At the end of the gene, RNA polymerase encounters a DNA sequence called a termination signal. RNA polymerase detaches from the DNA and releases the RNA molecule. 3 DNA RNA 4 Conclusion of transcription: After termination, the DNA completely rewinds into a double helix. The RNA molecule is free to move from the nucleus to the cytoplasm for translation, and RNA polymerase may move to another gene and begin transcription once again.

  17. RNA Transcription in Action gene growing RNA molecules end of gene DNA beginning of gene Fig. 12-4

  18. How Is the Base Sequence of Messenger RNA Translated into Protein? • Messenger RNA synthesis differs between prokaryotes and eukaryotes • Messenger RNA synthesis in prokaryotes • Genes for related functions are adjacent and are transcribed together • Because prokaryotes have no nuclear membrane, translation and transcription are not separated in space or time • As the mRNA molecule separates from the DNA, ribosomes immediately begin translating it to protein

  19. Messenger RNA Synthesis in Prokaryotic Cells Fig. 12-5 gene regulating DNA sequences gene 1 gene 2 gene 3 genes coding enzymes in a single metabolic pathway (a) Gene organization on a prokaryotic chromosome DNA mRNA ribosome direction of transcription RNA polymerase DNA mRNA protein ribosome (b) Simultaneous transcription and translation in prokaryotes

  20. How Is the Base Sequence of Messenger RNA Translated into Protein? • Messenger RNA synthesis in eukaryotes • In eukaryotes, the DNA is in the nucleus and the ribosomes are in the cytoplasm • The genes that encode the proteins for a metabolic pathway are not clustered together on the same chromosome • Each gene consists of two or more segments of DNA that encode for protein, called exons, that are interrupted by other segments that are not translated, called introns

  21. Messenger RNA Synthesis in Eukaryotic Cells Fig. 12-6 exons DNA promoter introns (a) Eukaryotic gene structure DNA 1 Transcription pre-mRNA An RNA cap and tail are added 2 cap tail 3 RNA splicing introns are cut out and broken down finished mRNA 4 Finished mRNA is moved to the cytoplasm for translation (b) RNA synthesis and processing in eukaryotes

  22. How Is the Base Sequence of Messenger RNA Translated into Protein? • Possible functions of intron-exon gene structure • Through alternative splicing of the exons in a gene, a cell can make multiple proteins from a single gene • Fragmented genes may provide a quick and efficient way for eukaryotes to evolve new proteins with new functions • If breaks in chromosomes occur in introns, exons may remain intact and be spliced to other chromosomes in ways that produce new, useful proteins

  23. How Is the Base Sequence of Messenger RNA Translated into Protein? • During translation, mRNA, tRNA, and ribosomes cooperate to synthesize proteins • Like transcription, translation has three steps • Initiation • Elongation • Termination

  24. Translation Is the Process of Protein Synthesis: Initiation Initiation: second tRNA binding site amino acid catalytic site met met met anticodon tRNA methionine tRNA large ribosomal subunit first tRNA binding site preinitiation complex A U C A U C mRNA A U C G C A U G G U U C A small ribosomal subunit U C G C A U G G U A start codon A tRNA with an attached methionine amino acid binds to a small ribosomal subunit, forming a preinitiation complex. 1 2 The large ribosomal subunit binds to the small subunit. The methionine tRNA binds to the first tRNA site on the large subunit. 3 The preinitiation complex binds to an mRNA molecule. The methionine (met) tRNA anticodon (UAC) base-pairs with the start codon (AUG) of the mRNA. Fig. 12-7 (1-3 of 9)

  25. Translation Is the Process of Protein Synthesis: Elongation Elongation: catalytic site met met initiator tRNA detaches met val peptide bond val val U A C U A C C A A C C A A A C U A A G C A U G G U U C A G C A U G G U U C A G C A U G G U U C A G U A ribosome moves one codon to the right 4 5 6 The catalytic site on the large subunit catalyzes the formation of a peptide bond linking the amino acids methionine and valine. The two amino acids are now attached to the tRNA in the second binding site. The "empty" tRNA is released and the ribosome moves down the mRNA, one codon to the right. The tRNA that is attached to the two amino acids is now in the first tRNA binding site and the second tRNA binding site is empty. The second codon of mRNA (GUU) base-pairs with the anticodon (CAA) of a second tRNA carrying the amino acid valine (val). This tRNA binds to the second tRNA site on the large subunit. Fig. 12-7 (4-6 of 9)

  26. Translation Is the Process of Protein Synthesis: Elongation and Termination Termination: met met val his val his met val his arg completed peptide arg C A A G U A C A A G U A ile stop codon G C A U G G U U C A G C A U G G U U C A G U A U A C G A A U C U A G U A A 7 8 9 The catalytic site forms a peptide bond between the amino acids, leaving them attached to the tRNA in the second binding site. The tRNA in the first site leaves, and the ribosome moves one codon over on the mRNA. This process repeats until a stop codon is reached; the mRNA and the completed peptide are released from the ribosome, and the subunits separate. The third codon of mRNA (CAU) base-pairs with the anticodon (GUA) of a tRNA carrying the amino acid histidine (his). This tRNA enters the second tRNA binding site on the large subunit. Fig. 12-7 (7-9 of 9)

  27. Complementary Base-Pairing Is Critical to the Process of Decoding Genetic Information gene (a) DNA A T G G G A G T T etc. complementary DNA strand template DNA strand etc. T A C C C T C A A codons A U G G G A G U U etc. (b) mRNA anticodons (c) tRNA U A C C C U C A A etc. amino acids (d) protein etc. methionine glycine valine Fig. 12-8

  28. Review • How is genetic material encoded in DNA and RNA? • Distinguish between transcription and translation. (define and locate)

  29. How Do Mutations Affect Protein Function? • Mutations are changes in the base sequence of DNA caused by mistakes during replication or by various environmental factors • Mutations take many forms and can affect protein function in many ways • Mutations fall into five categories • Inversions • Translocations • Deletions • Insertions • Substitutions

  30. How Do Mutations Affect Protein Function? • Inversionsand translocations • These mutations may be relatively benign if entire genes, including their promoter, are merely moved from one place to another • However, if a gene is split in two, it will no longer code for a complete, functional protein • Severe hemophilia is often caused by an inversion in the gene that encodes a protein required for blood clotting

  31. How Do Mutations Affect Protein Function? • Deletions and insertions • Depending on how many nucleotides are involved, deletions and insertions can cause a misreading of a gene’s codons during transcription or replication • The codons in THEDOGSAWTHECAT is changed by deletion of the letter “E” to THD OGS AWT HEC AT • Such mutations are called frameshift mutations

  32. How Do Mutations Affect Protein Function? • Deletions and insertions • Proteins that result from deletions and insertions have a very different amino acid sequence and almost always are nonfunctional • Deletions and insertions of three nucleotides (or a multiple of three) do not cause a shift of the reading frame and, so, may simply subtract or add a harmless amino acid to the protein

  33. How Do Mutations Affect Protein Function? • Point mutation (nucleotide substitution) • A point mutation sometimes does not change the amino acid sequence of the protein • Because many amino acids are encoded by more than one codon, the mutation may cause the same amino acid to be added • A known point mutation in the beta-globin gene for hemoglobin causes CTC to change to CTT, but since both codons code for glutamic acid, the protein is unchanged

  34. How Do Mutations Affect Protein Function? • Point mutation (nucleotide substitution) • A mutated protein mayfunction normally • In beta-globin, a point mutation of the CTC codon to GTC causes glutamic acid (hydrophilic) to be replaced with glutamine (also hydrophilic), but the resulting protein functions well

  35. How Do Mutations Affect Protein Function? • Point mutation (nucleotide substitution) • Some substitutions cause an altered amino acid sequence that change protein function dramatically, usually for the worse • The substitution of an adenine for a thymine in the CTC  CAC mutation in a hemoglobin gene causes valine (hydrophobic) to replace glutamic acid (hydrophilic) • Placing this hydrophobic amino acid on the outside of the hemoglobin molecule leads to the clumping of hemoglobin and distortion of the red blood cell seen in sickle cell anemia

  36. How Do Mutations Affect Protein Function? • Point mutation (nucleotide substitution) • The point mutation may introduce a premature stop codon, leading to an mRNA that produces an incomplete protein • Such a mutation in the beta-globin gene prevents production of functional beta-globin protein • This leads to beta-thalassemia • People with this mutation have only alpha-globin subunits and require frequent blood transfusions to survive because it doesn’t bind O2 as well.

  37. How Are Genes Regulated? • The human genome contains 20,000 to 30,000 genes • A given cell “expresses” (transcribes) only a small number of genes • Some genes are expressed in all cells, such as genes coding for RNAs, since all cells require proteins

  38. How Are Genes Regulated? • Other genes are expressed only in certain types of cells, at certain times in an organism’s life, or under specific environmental conditions • For example, even though every cell in your body contains the gene for casein, the major protein in milk, this gene is expressed only in certain cells in the breast, only in mature women, and only when a woman is breast-feeding

  39. How Are Genes Regulated? • Regulation of gene expression may occur at three different levels • Rate oftranscription, regulation determines which genes in a cell are expressed • Rate oftranslation, regulation determines how much protein is made from a particular type of mRNA • At the level of protein activity, regulation determines how long the protein lasts in a cell and how rapidly protein enzymes catalyze specific reactions • Although these general principles apply to both prokaryotic and eukaryotic organisms, there are some differences as well

  40. 12.5 How Are Genes Regulated? • In eukaryotic cells, transcriptional regulation occurs on at least three levels • The individual gene – promoters have several binding sites • Regions of chromosomes – too tightly wound • Entire chromosomes • In female mammals, one entire X chromosome is condensed (Barr bodies)

  41. How Are Genes Regulated? • In female mammals, one entire X chromosome is condensed • This effect can be observed in the fur patterns of calico cats • The X chromosome of a cat contains a gene for fur pigmentation • Different patches of skin cells in a cat inactivate different X chromosomes

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