Chapter 11. Gene Expression and Regulation. Lectures by Gregory Ahearn. University of North Florida. Copyright 2009 Pearson Education, Inc..

Transcription

1 Chapter 11 Gene Expression and Regulation Lectures by Gregory Ahearn University of North Florida Copyright 2009 Pearson Education, Inc..

2 11.1 How Is The Information In DNA Used In A Cell? Most genes contain information for the synthesis of a single protein. A gene is a stretch of DNA encoding the instructions for the synthesis of a single protein. Proteins form cellular structures and the enzymes that catalyze cellular chemical reactions.

3 11.1 How Is The Information In DNA Used In A Cell? Proteins are synthesized through the processes of transcription and translation. DNA does not directly guide protein synthesis, but rather, an intermediary ribonucleic acid (RNA) carries information from the nucleus to the cytoplasm.

4 11.1 How Is The Information In DNA Used In A Cell? RNA is different than DNA in three respects: RNA is single stranded; DNA is double stranded. RNA has the sugar ribose; DNA has deoxyribose. RNA contains the base uracil; DNA has thymine.

5 11.1 How Is The Information In DNA Used In A Cell?

6 11.1 How Is The Information In DNA Used In A Cell? Protein synthesis occurs in two steps, called transcription and translation. gene (a) Transcription messenger RNA DNA (nucleus) (cytoplasm) Transcription of the gene produces an mrna with a nucleotide sequence complementary to one of the DNA strands ribosome Translation of the mrna produces a protein molecule with an amino acid sequence determined by the nucleotide sequence in the mrna (b) Translation protein Fig. 11-1

7 11.1 How Is The Information In DNA Used In A Cell? Transcription: the information contained in the DNA of a specific gene is copied into one of three types of RNA Messenger RNA (mrna) Transfer RNA (trna) Ribosomal RNA (rrna) In eukaryotic cells, transcription occurs in the nucleus.

8 11.1 How Is The Information In DNA Used In A Cell? Translation: ribosomes convert the base sequence in mrna to the amino acid sequence of a protein In eukaryotic cells, translation occurs in the cytoplasm.

9 11.2 What Are The Functions Of RNA? Messenger RNA carries the code for a protein from the nucleus to the cytoplasm. All RNA is produced by transcription from DNA, but only mrna carries the code for amino acid sequence of a protein. mrna is synthesized in the nucleus and enters the cytoplasm through nuclear envelope pores. In the cytoplasm, mrna binds to ribosomes, which synthesize a protein specified by the mrna base sequence; DNA remains in the nucleus.

10 11.2 What Are The Functions Of RNA? Messenger RNA (mrna) A U G U G C G A G U U A (a) Messenger RNA (mrna) The base sequence of mrna carries the information for the amino acid sequence of a protein Fig. 11-2a

11 11.2 What Are The Functions Of RNA? Ribosomal RNA and proteins form ribosomes. Each ribosome consists of two subunits one small and one large. The small subunit has binding sites for mrna, a start trna, and other proteins that cooperate to read mrna to start protein synthesis. The large subunit has two binding sites for trna molecules, and one catalytic site where peptide bonds join amino acids together into a protein. During protein synthesis, the two subunits come together, clasping an mrna molecule between them.

12 11.2 What Are The Functions Of RNA? Ribosomal RNA (rrna) large subunit small subunit 1 2 catalytic site trna/amino acid binding sites rrna combines with proteins to form ribosomes; the small subunit binds mrna; the large subunit binds trna and catalyzes peptide bond formation between amino acids during protein synthesis (b) Ribosome: contains ribosomal RNA (rrna) Fig. 11-2b

13 11.2 What Are The Functions Of RNA? Transfer RNA molecules carry amino acids to the ribosomes. Each cell synthesizes many different kinds of transfer RNA, one or more for each amino acid. Twenty different kinds of enzymes in the cytoplasm, one for each amino acid, recognize the rrna and attach the correct amino acid. These loaded trna molecules deliver their amino acids to the ribosome, where they are incorporated into the growing protein chain.

14 11.2 What Are The Functions Of RNA? Transfer RNA (trna) trna (c) anticodon tyr Transfer RNA (trna) attached amino acid Each trna carries a specific amino acid (in this example, tyrosine [tyr]) to a ribosome during protein synthesis; the anticodon of trna pairs with a codon of mrna, ensuring that the correct amino acid is incorporated into the protein Fig. 11-2c

15 11.3 What Is The Genetic Code? The genetic code translates the sequence of bases in nucleic acids into the sequence of amino acids in proteins. A sequence of three bases codes for an amino acid; the triplet is called a codon. There are 64 possible combinations of codons, which is more than enough to code for the 20 amino acids in proteins.

16 11.3 What Is The Genetic Code?

17 11.3 What Is The Genetic Code? How does a cell recognize where codons start and stop, and where the code for an entire proteins starts and stops? Most codons specify a specific amino acid in a protein sequence, but others are punctuation marks that indicate the end of one protein sequence and the start of another. All proteins begin with the start codon AUG (methionine), and all end with UAG, UAA, or UGA, called stop codons. Almost all amino acids are coded for by more than one codon (e.g., six codons code for leucine).

18 11.4 How Is The Information In A Gene Transcribed Into RNA? Transcription copies the genetic information of DNA into RNA in the nucleus of eukaryotic cells. Transcription is made up of three different processes: Initiation: the promotor region at the beginning of a gene starts transcription Elongation: the main body of a gene is where the RNA strand is elongated Termination: the termination signal at end of a gene is where RNA synthesis stops

19 11.4 How Is The Information In A Gene Transcribed Into RNA? Transcription begins when RNA polymerase binds to the promotor of a gene. RNA polymerase catalyzes the transcription of DNA to RNA. RNA polymerase first finds the promoter region (a non-transcribed sequence of DNA bases) that marks the start of a gene, and then binds to it, opening up the DNA as it does. Transcription of the gene begins after the promoter is bound to RNA polymerase.

20 11.4 How Is The Information In A Gene Transcribed Into RNA? Initiation DNA gene 1 gene 2 gene 3 RNA polymerase DNA promoter Initiation: RNA polymerase binds to the promoter region of DNA near the beginning of a gene, separating the double helix near the promoter. Fig. 11-3(1)

21 11.4 How Is The Information In A Gene Transcribed Into RNA? Elongation generates a growing strand of RNA. RNA polymerase adds complementary bases to those in the DNA template strand, to make a growing RNA strand that has uracil rather than thymine complementary to adenine. The two strands of DNA re-form the original double helix. One end of the growing RNA strand drifts away from the DNA molecule, while the other remains attached to the DNA template strand by the RNA polymerase.

22 11.4 How Is The Information In A Gene Transcribed Into RNA? 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. Fig. 11-3(2)

23 11.4 How Is The Information In A Gene Transcribed Into RNA? RNA transcription in action gene DNA growing RNA molecules end of gene beginning of gene Fig. 11-4

24 11.4 How Is The Information In A Gene Transcribed Into RNA? Transcription stops when RNA polymerase reaches the termination signal. RNA polymerase continues along the DNA template strand until it comes to the termination signal (a specific sequence of DNA bases). At the termination signal, RNA polymerase drops off the DNA and releases the completed RNA molecule. The enzyme is ready to bind to another promoter, to start the process over.

25 11.4 How Is The Information In A Gene Transcribed Into RNA? Termination 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. Fig. 11-3(3)

26 11.4 How Is The Information In A Gene Transcribed Into RNA? Conclusion of transcription RNA 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. Fig. 11-3(4)

27 11.4 How Is The Information In A Gene Transcribed Into RNA? Transcription is selective. Some genes are transcribed in all cells because they encode essential proteins, like the electron transport chain of mitochondria. Other genes are transcribed only in specific types of cells.

28 11.4 How Is The Information In A Gene Transcribed Into RNA? Transcription is selective (continued). How do cells regulate which genes are transcribed? Proteins bind to control regions near gene promotors and block or enhance the binding of RNA polymerase. By this means, the amount of a specific protein encoded by a specific gene in a cell can be controlled.

29 11.5 How Is The Information In Messenger RNA Translated Into Protein? mrna, with a specific base sequence, is used during translation to direct the synthesis of a protein with the amino acid sequence encoded by the mrna. Decoding the base sequence of mrna is the job of trna and ribosomes in the cytoplasm. The ability of trna to deliver the correct amino acid to the ribosomes depends on base pairing between each codon of mrna and a set of three complementary bases in trna, called the anticodon.

30 11.5 How Is The Information In Messenger RNA Translated Into Protein? Like transcription, translation has three steps: Initiation of protein synthesis Elongation of the protein chain Termination of translation

31 11.5 How Is The Information In Messenger RNA Translated Into Protein? Initiation: translation begins when trna and mrna bind to a ribosome The first amino acid in all proteins is a methionine (AUG codon). An initiation complex a small ribosomal subunit, a methonine trna, and a methionine amino acid binds to an AUG codon in an mrna molecule. The large subunit of the ribosome joins the complex to complete the assembly of the ribosome. The methionine trna binds to the first binding site on the large ribosome subunit.

32 11.5 How Is The Information In Messenger RNA Translated Into Protein? Initiation Initiation: initiation complex met U A C amino acid small ribosomal subunit methionine trna A trna with an attached methionine amino acid binds to a small ribosomal subunit, forming an initiation complex. mrna trna met U A C anticodon G C A U G G U U C A start codon The initiation complex binds to an mrna molecule. The methionine (met) trna anticodon (UAC) base-pairs with the start codon (AUG) of the mrna. catalytic site first trna binding site second trna binding site met U A C G C A U G G U U C A large ribosomal subunit The large ribosomal subunit binds to the small subunit. The methionine trna binds to the first trna site on the large subunit. Fig. 11-5(1,2,3)

33 11.5 How Is The Information In Messenger RNA Translated Into Protein? Elongation: amino acids are added one at a time to the growing protein chain Assembled ribosomes have two binding sites and a catalytic site. The first binding site has methionine and its rrna attached. The second binding site accepts another trna with an anticodon complementary to the codon on the mrna associated with the second binding site.

34 11.5 How Is The Information In Messenger RNA Translated Into Protein? Elongation Elongation: met val catalytic site met val peptide bond initiator trna detaches met val U A C C A A U A C C A A C 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 U A G 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. 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. ribosome moves one codon to the right 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. Fig. 11-5(4,5,6)

35 11.5 How Is The Information In Messenger RNA Translated Into Protein? Elongation (continued) The catalytic site forms a peptide bond between the two amino acids. The ribosome moves to the next codon on mrna and shifts the growing amino acid chain from the second to the first binding site. The third amino acid is then added to the chain. The ribosome moves along mrna, adding one amino acid to the next. The process repeats over and over as the ribosome moves along the mrna, one codon at a time.

36 11.5 How Is The Information In Messenger RNA Translated Into Protein? Elongation (continued) met val his met val his C A A G U A C A A G U A G C A U G G U U C A U A G G C A U G G U U C A U A G 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. The catalytic site forms a peptide bond between valine and histidine, leaving the peptide 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. Fig. 11-5(7,8)

37 11.5 How Is The Information In Messenger RNA Translated Into Protein? Termination: a stop codon signals the end of translation Ribosome encounters a stop codon in the mrna sequence that signals that protein synthesis is complete. Stop codons do not bind trna, but rather, they bind proteins that cause the ribosome to release the complete amino acid chain. The large and small subunits of the ribosome also come apart once the stop codon is reached.

38 11.5 How Is The Information In Messenger RNA Translated Into Protein? Termination Termination: met val completed peptide his arg arg ile stop codon C G A A U C U A G U A A This process repeats until a stop codon is reached; the mrna and the completed peptide are released from the ribosome, and the subunits separate. Fig. 11-5(9)

39 11.5 How Is The Information In Messenger RNA Translated Into Protein? Summing up: transcription and translation With a few exceptions, each gene codes for a single protein. Transcription of a protein-coding gene produces an mrna that is complementary to the template strand of the DNA for the gene. Enzymes in the cytoplasm attach the appropriate amino acid to each trna. The mrna moves from the nucleus to the cytoplasm. trnas carry their attached amino acids to the ribosome.

40 11.5 How Is The Information In Messenger RNA Translated Into Protein? Summing up: transcription and translation (continued) At the ribosome, the bases in trna anticodons bind to the complementary bases in mrna codons. The amino acids attached to the trnas line up in the sequence specified by the codons. The ribosome joins the amino acids together with peptide bonds to form a protein. When a stop codon is reached, the finished protein is released from the ribosome.

41 11.5 How Is The Information In Messenger RNA Translated Into Protein? Complementary base pairing is critical to decoding genetic information. (a) DNA complementary DNA strand template DNA strand gene A T G G G A G T T T A C C C T C A A codons etc. etc. (b) mrna A U G G G A G U U etc. anticodons (c) trna U A C C C U C A A etc. amino acids (d) protein methionine glycine valine etc. Fig. 11-6

42 11.6 How Do Mutations Affect Gene Function? Changes in the sequence of DNA nucleotide bases as a result of replication errors, ultraviolet light, chemicals, and many other environmental factors are called mutations. Sometimes during DNA replication, an incorrect pair of nucleotides is incorporated into the growing DNA double helix. This is called nucleotide substitution, or point mutation, because the nucleotides in the DNA sequence are changed.

43 11.6 How Do Mutations Affect Gene Function? Mutations (continued) A insertion mutation occurs when one or more new nucleotide pairs are inserted into a gene. A deletion mutation occurs when one or more nucleotide pairs are removed from a gene.

44 11.6 How Do Mutations Affect Gene Function? Mutations may have a variety of effects on protein structure and function. The protein may be unchanged. The new protein may be functionally equivalent to the original one. Protein function may be changed by an altered amino acid sequence. Protein function may be destroyed by a premature stop codon.

45 11.6 How Do Mutations Affect Gene Function?

46 11.6 How Do Mutations Affect Gene Function? Mutations are the raw material for evolution. Mutations are the ultimate source of all genetic differences among individuals. Without mutations, individuals would share the same DNA sequence. Most mutations are harmful; some improve the individual s ability to survive and reproduce. The mutation may be passed from generation to generation and become more common over time. This process is known as natural selection, and is the major cause of evolutionary change.

47 11.7 Are All Genes Expressed? All of the genes in the human genome are present in each body cell, but individual cells express only a small fraction of them. The particular set of genes that is expressed depends on the type of cell and the needs of the organism. This regulation of gene expression is crucial for proper functioning of individual cells and entire organisms.

48 11.7 Are All Genes Expressed? Gene expression differs from cell to cell and over time. The set of genes that are expressed depends on the function of a particular cell. Hair cells synthesize the protein keratin, while muscle cells make the proteins actin and myosin but do not make keratin. A human male does not express a casein gene, the protein in human milk, but will pass on the gene for casein synthesis to his daughter, who will express it if she bears children.

49 11.7 Are All Genes Expressed? Environmental cues influence gene expression. Changes in an organism s environment help determine which genes are transcribed. Longer spring days stimulate the sex organs of birds to enlarge and produce sex hormones. These hormones cause the birds to produce eggs and sperm, to mate, and to build nests. All these changes result directly or indirectly from alterations in gene expression.

50 11.8 How Is Gene Expression Regulated? A cell may regulate gene expression in many different ways. It may alter the rate of transcription of mrna. It may affect how long a given mrna molecule lasts before being broken down. It may affect how fast the mrna is translated into protein. It may affect how long the protein lasts, or how fast a protein enzyme catalyzes a reaction.

51 11.8 How Is Gene Expression Regulated? Regulatory proteins that bind to promoters alter the transcription of genes. Many steroid hormones act in this way. In birds, estrogen enters cells of the female reproductive system and binds to a receptor protein during the breeding season. The estrogen receptor combination then binds to the DNA in a region near the promotor of an albumen gene.

52 11.8 How Is Gene Expression Regulated? Regulatory proteins that bind to promoters alter the transcription of genes (continued). This attachment makes it easier for RNA polymerase to bind to the promotor and to transcribe large amounts of albumen mrna, which is translated into the albumin protein needed to make eggs.

53 11.8 How Is Gene Expression Regulated? Some regions of chromosomes are condensed and not normally transcribed. Certain parts of eukaryotic chromosomes are in a highly condensed, compact state in which most of the DNA is inaccessible to RNA polymerase. Some of these tightly condensed regions may contain genes that are not currently being transcribed, but when those genes are needed, the portion of the chromosome containing those genes becomes decondensed so that transcription can occur.

54 11.8 How Is Gene Expression Regulated? Entire chromosomes may be inactivated and not transcribed. In some cases, almost an entire chromosome may be condensed, making it largely inaccessible to RNA polymerase. In human females, one of their two X chromosomes may become inactivated by a special coating of RNA called Xist, which condenses the chromosome and prevents gene transcription.

55 11.8 How Is Gene Expression Regulated? The condensed X chromosome shows up in the nucleus as a dark spot called the Barr body. Fig. 11-7