1.
Gene Expression and Regulation

2.
The Link Between DNA and Protein <ul><li>DNA contains the molecular blueprint of every cell </li></ul><ul><li>Proteins are the “molecular workers” of the cell </li></ul><ul><li>Proteins control cell shape, function, reproduction, and synthesis of biomolecules </li></ul><ul><li>The information in DNA genes must therefore be linked to the proteins that run the cell </li></ul>

3.
One Gene Encodes One Protein <ul><li>Synthesis of new molecules inside the cell occurs through biochemical pathways </li></ul><ul><li>Each step in a biochemical pathway is catalyzed by a protein enzyme </li></ul><ul><li>George Beadle and Edward Tatum showed that one DNA gene encodes the information for one enzyme (protein) in a biochemical pathway </li></ul><ul><ul><li>There are exceptions to the one gene/one protein relationship, as discussed later </li></ul></ul>

4.
RNA Intermediaries <ul><li>DNA in eukaryotes is kept in the nucleus </li></ul><ul><li>Protein synthesis occurs at ribosomes in the cytoplasm </li></ul><ul><li>DNA information must be carried by an intermediary ( RNA ) from nucleus to cytoplasm </li></ul>

6.
Three Types of RNA catalytic site tRNA docking sites Attached amino acid tRNA transfer Small subunit rRNA ribosomal mRNA Large subunit mRNA messenger Met anticodon 1 2 C A G A U G G A G U U A U G G A G U

7.
Transcription and Translation <ul><li>DNA directs protein synthesis in a two-step process </li></ul><ul><ul><li>Information in a DNA gene is copied into mRNA in the process of transcription </li></ul></ul><ul><ul><li>2. mRNA, together with tRNA, amino acids, and a ribosome , synthesize a protein in the process of translation </li></ul></ul>

8.
Information Flow: DNA  RNA  Protein

9.
The Genetic Code <ul><li>The base sequence in a DNA gene dictates the sequence and type of amino acids in translation </li></ul><ul><li>Bases in mRNA are read by the ribosome in triplets called codons </li></ul><ul><li>Each codon specifies a unique amino acid in the genetic code </li></ul><ul><li>Each mRNA also has a start and a stop codon </li></ul>

11.
Cracking the genetic code a. b. c. d.

12.
Overview of Transcription <ul><li>Transcription of a DNA gene into RNA has three stages </li></ul><ul><ul><li>Initiation </li></ul></ul><ul><ul><li>Elongation </li></ul></ul><ul><ul><li>Termination </li></ul></ul>

13.
Initiation <ul><li>Initiation phase of transcription </li></ul><ul><ul><li>DNA molecule is unwound and strands are separated at the beginning of the gene sequence </li></ul></ul><ul><ul><li>2. RNA polymerase binds to promoter region at beginning of a gene on template strand </li></ul></ul>

15.
Elongation <ul><li>Elongation phase of transcription </li></ul><ul><ul><li>RNA polymerase synthesizes a sequence of RNA nucleotides along DNA template strand </li></ul></ul><ul><ul><li>2. Bases in newly synthesized RNA strand are complementary to the DNA template strand </li></ul></ul><ul><ul><li>RNA strand peels away from DNA template strand as DNA strands repair and wind up </li></ul></ul>

17.
Elongation <ul><li>As elongation proceeds, one end of the RNA drifts away from the DNA; RNA polymerase keeps the other end temporarily attached to the DNA template strand </li></ul><ul><li>Figure 10-5 , p. 174, shows many RNA molecules undergoing elongation </li></ul>

19.
Termination <ul><li>Termination phase of transcription </li></ul><ul><ul><li>RNA polymerase reaches a termination sequence and releases completed RNA strand </li></ul></ul>

22.
mRNA <ul><li>An intermediate molecule is required to convey DNA gene sequence to the ribosome </li></ul><ul><li>Messenger RNA (mRNA) performs this function by serving as the complementary copy of a DNA gene that is read by a ribosome </li></ul>

23.
mRNA <ul><ul><li>In prokaryotes </li></ul></ul><ul><ul><li>The chromosomes are not contained within a nucleus </li></ul></ul><ul><ul><li>All of the nucleotides in a gene encode for the amino acids of a protein </li></ul></ul><ul><ul><li>Genes for a related function are adjacent and are transcribed together </li></ul></ul><ul><ul><li>Transcription and translation occur simultaneously within the same compartment </li></ul></ul>

27.
mRNA <ul><ul><li>In eukaryotes </li></ul></ul><ul><ul><li>The DNA is in the nucleus and the ribosomes are in the cytoplasm </li></ul></ul><ul><ul><li>The genes that encode the proteins for a biochemical pathway are not clustered together on the same chromosome </li></ul></ul><ul><ul><ul><li>Each gene consists of multiple segments of DNA that encode for protein, called exons </li></ul></ul></ul><ul><ul><ul><li>Exons are interrupted by other segments that are not translated, called introns </li></ul></ul></ul>

28.
Introns snipped out Introns snipped out exons DNA introns promoter Initial transcript Splicing completed mRNA transcript Transcription from DNA to RNA

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mRNA <ul><ul><li>In eukaryotes (continued) </li></ul></ul><ul><ul><li>Transcription of a gene produces a very long RNA strand that contains introns and exons </li></ul></ul><ul><ul><li>Enzymes in the nucleus cut out the introns and splice together the exons to make true mRNA </li></ul></ul><ul><ul><li>mRNA exits the nucleus through a membrane pore and associates with a ribosome </li></ul></ul>

30.
Ribosomes <ul><li>Ribosomes are large complexes of proteins and rRNA </li></ul>

31.
Ribosomes <ul><li>Ribosomes are composed of two subunits </li></ul><ul><ul><li>Small subunit has binding sites for mRNA and a tRNA </li></ul></ul><ul><ul><li>Large subunit has binding sites for two tRNA molecules and catalytic site for peptide bond formation </li></ul></ul>

32.
Transfer RNAs <ul><li>Transfer RNAs hook up to and bring amino acids to the ribosome </li></ul><ul><li>There is at least one type of tRNA assigned to carry each of the twenty different amino acids </li></ul><ul><li>Each tRNA has three exposed bases called an anticodon </li></ul><ul><li>The bases of the tRNA anticodon pair with an mRNA codon within a ribosome binding site </li></ul>

33.
Translation <ul><li>Ribosomes, tRNA, and mRNA cooperate in protein synthesis, which begins with initiation: </li></ul><ul><ul><li>The mRNA binds to the small ribosomal subunit </li></ul></ul><ul><ul><li>2. The mRNA slides through the subunit until the first AUG (start codon) is exposed in the first tRNA binding site… </li></ul></ul>

34.
Translation <ul><ul><li>3. The first tRNA carrying methionine (and anticodon UAC) binds to the mRNA start codon completing the initiation complex </li></ul></ul><ul><ul><li>4. The large ribosomal subunit joins the complex </li></ul></ul>

35.
Translation: Initiation (1) A tRNA with an attached methionine amino acid binds to a small ribosomal subunit, forming an initiation complex.

36.
Translation: Initiation (2) The initiation complex binds to end of mRNA and travels down until it encounters an AUG codon in the mRNA. The anticodon of the tRNA in the initiation complex forms base pairs with the AUG codon.

37.
Translation: Initiation (3) The large ribosomal subunit binds to the small subunit, with the mRNA between the two subunits. The methionine tRNA is in the first tRNA site on the large subunit.

38.
Translation: Elongation 1 The second tRNA enters the second tRNA site on the large ribosomal subunit. Which tRNA binds depends on the ability of its anticodon (CAA in this example) to base pair with the codon (GUU in this example) in the mRNA. tRNAs with a CAA anticodon carry an attached valine amino acid, which was added to it by enzymes in the cytoplasm.

39.
Translation: Elongation 2 The &quot;empty&quot; 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.

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Translation: Elongation 3 The catalytic site on the large subunit catalyzes the formation of a peptide bond linking the amino acids methionine to valine. The two amino acids are now attached to the tRNA in the second binding position.

41.
Translation: Elongation 4 Another tRNA enters the second tRNA binding site carrying its attached amino acid. The tRNA has an anticodon that pairs with the codon. (Here, the CAU mRNA codon pairs with a GUA tRNA anticodon.) The tRNA molecule carries the amino acid histidine (his).

42.
Translation: Elongation 5 Binding of tRNAs, & formation of peptide bonds continues. Ribosome reaches STOP codon (UAG). Protein &quot;release factors&quot; signal the ribosome to release the protein. The mRNA is also released and large & small subunits separate.

43.
Translation: Termination The catalytic site forms a new peptide bond, in this example, between the valine and the histidine. A three-amino acid chain is now attached to the tRNA in the second tRNA binding site. The empty tRNA in the first site is released and the ribosome moves one codon to the right.

44.
Complementary Base Pairing Methionine Glycine Valine etc. template DNA strand (a) complementary DNA strand (b) mRNA (c) tRNA (d) protein amino acids anticodons codons gene etc. etc. etc. etc. G G G A G C G A U U U C A A C A U C C U G G G A G T T C T G A G T C C C C A A A T C

45.
Overview of Information Flow Amino Acids Active Protein Inactive Protein (Cytoplasm) DNA (Nucleus) rRNA tRNA 1 Transcription + Proteins Ribosomes tRNA tRNA-AA mRNA mRNA 2 Translation 3 Modification Product Substrate 4 Degradation

46.
Effects of Mutations on Proteins <ul><li>Recall that mutations are changes in the base sequence of DNA </li></ul><ul><li>Most mutations are categorized as </li></ul><ul><ul><li>Substitutions </li></ul></ul><ul><ul><li>Deletions </li></ul></ul><ul><ul><li>Insertions </li></ul></ul><ul><ul><li>Inversions </li></ul></ul><ul><ul><li>Translocations </li></ul></ul>

47.
Effects of Mutations on Proteins <ul><li>Inversions and translocations </li></ul><ul><ul><li>When pieces of DNA are broken apart and reattached in different orientation or location </li></ul></ul><ul><ul><li>Not problematic if entire gene is moved </li></ul></ul><ul><ul><li>If gene is split in two it will no longer code for a complete, functional protein </li></ul></ul>

48.
Effects of Mutations on Proteins <ul><li>Insertions or deletions </li></ul><ul><ul><li>Nucleotides are added or subtracted from a gene </li></ul></ul><ul><ul><li>Reading frame of RNA codons is changed </li></ul></ul><ul><ul><ul><li>THEDOGSAWTHECAT is changed by deletion of the letter “S” to THEDOGAWTHECAT </li></ul></ul></ul><ul><ul><li>Resultant protein has very different amino acid sequence; almost always is non-functional </li></ul></ul>

49.
Effects of Mutations on Proteins <ul><li>Nucleotide substitutions (point mutations) </li></ul><ul><ul><li>An incorrect nucleotide takes the place of a correct one </li></ul></ul><ul><ul><li>Protein structure and function is unchanged because many amino acids are encoded by multiple codons </li></ul></ul><ul><ul><li>Protein may have amino acid changes that are unimportant to function ( neutral mutations ) </li></ul></ul>

50.
Effects of Mutations on Proteins <ul><li>Effects of nucleotide substitutions </li></ul><ul><ul><li>Protein function is changed by an altered amino acid sequence (as in gly  val in hemoglobin in sickle cell anemia) </li></ul></ul><ul><ul><li>Protein function is destroyed because DNA mutation creates a premature stop codon </li></ul></ul>

52.
Mutations Fuel Evolution <ul><li>Mutations are heritable changes in the DNA </li></ul><ul><li>Approx. 1 in 10 5 -10 6 eggs or sperm carry a mutation </li></ul><ul><li>Most mutations are harmful or neutral </li></ul><ul><li>Mutations create new gene sequences and are the ultimate source of genetic variation </li></ul><ul><li>Mutant gene sequences that are beneficial may spread through a population and become common </li></ul>

53.
How Are Genes Regulated? <ul><li>The human genome contains ~ 30,000 genes </li></ul><ul><li>A given cell “expresses” (transcribes) only a small number of genes </li></ul><ul><li>Some genes are expressed in all cells </li></ul><ul><li>Other genes are expressed only </li></ul><ul><ul><li>In certain types of cells </li></ul></ul><ul><ul><li>At certain times in an organism’s life </li></ul></ul><ul><ul><li>Under specific environmental conditions </li></ul></ul>

54.
Gene Regulation in Prokaryotes <ul><li>Prokaryotic DNA is organized into units called operons, which contain functionally related genes </li></ul>

55.
Gene Regulation in Prokaryotes <ul><li>Each operon consists of </li></ul><ul><ul><li>A regulatory gene , which controls the transcription of other genes </li></ul></ul><ul><ul><li>A promoter , which RNA polymerase recognizes as the place to start transcribing </li></ul></ul><ul><ul><li>An operator , which governs access of RNA polymerase to the promoter </li></ul></ul><ul><ul><li>The structural genes , which encode for related proteins </li></ul></ul>

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Gene Regulation in Prokaryotes <ul><li>Whole operons are regulated as units, so that functionally related proteins are synthesized simultaneously when the need arises </li></ul>

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Gene Regulation in Prokaryotes <ul><li>The intestinal bacterium Escherichia coli (E.coli) lives on what its host eats </li></ul><ul><li>Specific enzymes are needed to metabolize the type of food that comes along </li></ul><ul><li>e.g. in newborn mammals, E.coli are bathed in milk, containing the milk sugar lactose </li></ul><ul><li>The lactose operon contains three structural genes, each coding for an enzyme that aids in lactose metabolism </li></ul>

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Gene Regulation in Prokaryotes <ul><li>Figure 10-10 , p. 181, illustrates regulation of the lactose operon… </li></ul>

62.
Gene Regulation in Eukaryotes <ul><li>Eukaryotic gene regulation </li></ul><ul><ul><li>DNA is in a membrane-bound nucleus </li></ul></ul><ul><ul><li>Variety of cell types in multicelluar eukaryotes </li></ul></ul><ul><ul><li>The genome is organized differently </li></ul></ul><ul><ul><li>RNA transcripts undergo complex processing </li></ul></ul>

63.
Gene Regulation in Eukaryotes <ul><li>Expression of genetic information by a eukaryotic cell is a multistep process, beginning with transcription of DNA, and ending with a protein that performs a particular function </li></ul>

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Gene Regulation in Eukaryotes <ul><li>Gene expression is regulated in a number of ways </li></ul><ul><ul><li>The frequency of transcription of a gene can be controlled </li></ul></ul><ul><ul><li>Different mRNAs may be translated at different rates </li></ul></ul><ul><ul><li>Proteins may be synthesized in an inactive form and require modification for activation </li></ul></ul><ul><ul><li>Life span of a protein can be regulated </li></ul></ul>

66.
Gene Regulation in Eukaryotes <ul><li>In eukaryotic cells, transcriptional regulation occurs on at least three levels </li></ul><ul><ul><li>The individual gene </li></ul></ul><ul><ul><li>Regions of chromosomes </li></ul></ul><ul><ul><li>Entire chromosomes </li></ul></ul>

67.
Gene Regulation in Eukaryotes <ul><li>Regulatory proteins can bind to a gene’s promoter region and alter transcription </li></ul><ul><ul><li>The protein hormone estrogen causes binding of a protein to certain gene promoters, activating transcription </li></ul></ul>

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Gene Regulation in Eukaryotes Condensed or tightly wound DNA can make genes inaccessible to RNA polymerase Whole chromosomes can be condensed and inactivated (e.g. Barr bodies in female mammals)

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The End