HOW GENES WORK CHAPTER 12 THE CENTRAL DOGMA • The path of information is often referred to as the central dogma. DNA RNA protein THE CENTRAL DOGMA • The use of information in DNA to direct the production of particular proteins is called gene expression, which takes place in two stages. • Transcription is the process when a messenger RNA (mRNA) is made from a gene within the DNA. • Translation is the process of using the mRNA to direct the production of a protein. TRANSCRIPTION • The information contained in DNA is stored in blocks called genes. • The genes code for proteins. • The proteins determine what a cell will be like. TRANSCRIPTION • The DNA stores this information safely in the nucleus where it never leaves. • Instructions are copied from the DNA into messages comprised of RNA. • These messages are sent out into the cell to direct the assembly of proteins. Nucleus DNA Transcription mRNA Nuclear envelope Protein Cytoplasm Translation TRANSCRIPTION • A protein called RNA polymerase produces the mRNA copy of DNA during transcription. • It first binds to one strand of the DNA at a site called the promoter and then moves down the DNA molecule and assembles a complementary copy of RNA • RNA uses uracil (U) instead of thymine (T) TRANSCRIPTION Coding strand Unwinding Template strand 3′ 5′ A T T T A A G C T A C G A C A G T G A C T C G T 3′ A T U G C U A C A C G A T G G C T A A C T G 3′ A G Rewinding U C A RNA-DNA hybrid helix 5′ G T RNA polymerase http://www.dnalc.org/resources/3d/12-transcription-basic.html 5′ mRNA DNA GENE EXPRESSION • The prokaryotic gene is an uninterrupted stretch of DNA nucleotides that corresponds to proteins. • In eukaryotes, the coding portions of the DNA nucleotide sequence are interrupted by noncoding sections of DNA. • The coding portions are known as exons while the noncoding portions are known as introns. GENE EXPRESSION • When a eukaryotic cell first transcribes a gene, it produces a primary RNA transcript of the entire gene. • The primary transcript is then processed in the nucleus. • Enzyme-RNA complexes cut out the introns and join together the exons to form a shorter mRNA transcript. • The sequences of the introns (90% of typical human gene) are not translated. • A 5’ cap and a 3’ poly-A tail are also added. GENE EXPRESSION Exon (coding region) DNA 5′ cap Primary RNA transcript Mature mRNA transcript Intron (noncoding region) 1 2 3 4 5 6 Transcription Introns are cut out and coding regions are spliced together http://www.dnalc.org/resources/3d/rna-splicing.html 7 3′ poly-A tail TRANSLATION • To correctly read a gene, a cell must translate the information encoded in the DNA (nucleotides) into the language of proteins (amino acids). • Translation follows rules set out by the genetic code. • The mRNA is “read” in three-nucleotide units called codons. • Each codon corresponds to a particular amino acid. TRANSLATION • The genetic code was determined from trialand-error experiments to work out which codons matched with which amino acids. • The genetic code is universal and employed by all living things. THE GENETIC CODE (RNA CODONS) The Genetic Code Second Letter First Letter U C A G U C A UUU Phenylalanine UUC UUA Leucine UUG UCU UCC UCA UCG UAU UAC UAA UAG CUU CUC Leucine CUA CUG CCU CCC CCA CCG AUU AUC AUA AUG ACU ACC ACA ACG Isoleucine Methionine; Start GUU GUC Valine GUA GUG GCU GCC GCA GCG Serine Proline Threonine Alanine CAU CAC CAA CAG AAU AAC AAA AAG GAU GAC GAA GAG Third Letter G Tyrosine Stop Stop Histidine Glutamine Asparagine Lysine Aspartate Glutamate UGU UGC UGA UGG CGU CGC CGA CGG AGU AGC AGA AGG GGU GGC GGA GGG Cysteine Stop Tryptophan Arginine Serine Arginine Glycine There are 64 different codons in the genetic code. U C A G U C A G U C A G U C A G TRANSLATION • Translation occurs in ribosomes, which are the protein-making factories of the cell • Each ribosome is a complex of proteins and several segments of ribosomal RNA (rRNA). • Ribosomes are comprised of two subunits: • Small subunit • Large subunit TRANSLATION • The small subunit has a short sequence of rRNA exposed that is identical to a leader sequence that begins all genes. • mRNA binds to the small subunit. TRANSLATION Large • The large RNA subunit has three subunit binding sites for transfer RNA (tRNA) located directly Small subunit adjacent to the exposed rRNA sequence on the small subunit. Large ribosomal subunitP site E site A site E P A mRNA binding site Small ribosomal subunit • These binding sites are called the A, P, and E sites. • It is the tRNA molecules that bring amino acids to the ribosome to use in making proteins. TRANSLATION • The structure of a tRNA molecule is important to its function. • It has an amino acid attachment site at one end and a three-nucleotide sequence at the other end. TRANSLATION • This threenucleotide sequence is called the anticodon and is complementary to 1 of the 64 codons of the genetic code. • Activating enzymes match amino acids with their proper tRNAs. 3′ OH Amino acid attaches here 5′ 5′ 3′ Anticodon Anticodon TRANSLATION • Once an mRNA molecule has bound to the small ribosomal subunit, the other larger ribosomal subunit binds as well, forming a complete ribosome. • During translation, the mRNA threads through the ribosome three nucleotides at a time. • A new tRNA holding an amino acid to be added enters the ribosome at the A site. TRANSLATION • Before a new tRNA can be added, the previous tRNA in the A site shifts to the P site. • At the P site, peptide bonds form between the incoming amino acid and the growing chain of amino acids. • The now empty tRNA in the P site eventually shifts to the E site where it is released. KEY BIOLOGICAL PROCESS: TRANSLATION 1 2 Amino acid Met 3 4 Leu Asn tRNA P site Met Met Leu A site Leu Asn Anticodon E site U A C A U G C U G A A U Met Leu mRNA Ribosome The initial tRNA occupies the P site on the ribosome. Subsequent tRNAs with bound amino acids first enter the ribosome at the A site. U A C G A C A U G C U G A A U A C U A C G G A A U A U G C U G A C U U A A U G C U G A A U Codon The tRNA that binds to the A site has an anticodon complementary to the codon on them RNA. The ribosome moves three nucleotides to the right as the initial amino acid is transferred to the second amino acid at the P site. http://www.dnalc.org/resources/3d/15-translation-basic.html The initiating tRNA leaves the ribosome at the E site, and the next tRNA enters at the A site. TRANSLATION • Translation continues until a “stop” codon is encountered that signals the end of the protein. • The ribosome then falls apart and the newly made protein is released into the cell. Growing polypeptide chain Amino acid tRNA 5′ Ribosome mRNA 3′ GENE EXPRESSION • Gene expression works the same way in all organisms. DNA Replication Key starting materials Process Key end product DNA polymerase Two DNA duplexes DNA Helicase Ligase Transcription Key starting materials Process Key end product DNA mRNA RNA polymerase Translation Key starting materials Process Key end product tRNA Amino acids mRNA Ribosome Polypeptide GENE EXPRESSION • In prokaryotes, a gene can be translated as it is transcribed. • In eukaryotes, a nuclear membrane separates the processes of transcription and translation, making protein synthesis much more complicated. Amino acid 6 The amino acid chain grows until the polypeptide is completed. Completed polypeptide 5′ Ribosome moves toward 3′ end Cytoplasm 5 tRNAs bring their amino acids in at the A site on the ribosome. Peptide bonds form between amino acids at the P site,and tRNAs exit the ribosome from the E site. Ribosome 4 tRNA molecules become attached to specific amino acids with the help of activating enzymes. Amino acids are brought to the ribosome in the order directed by the mRNA. Nuclear membrane DNA 3′ 3′ RNA polymerase In the cell nucleus, RNA polymerase transcribes RNA from DNA. 3′ 5′ Primary RNA transcript ribosomal subunit 5′ 3′ Exons Poly-A tail Introns 3′ Cap Cap Nuclear pore Small 5′ 1 5′ 3′ mRNA Large ribosomal subunit Poly-A tail 5′ mRNA 2 Introns are excised from the RNA transcript, and the remaining exons are spliced together, producing mRNA. 3 mRNA is transported out of the nucleus. In the cytoplasm, ribosomal subunits bind to the mRNA TRANSCRIPTIONAL CONTROL IN PROKARYOTES RNA • An operon is a segment of DNA Repressor polymerase containing a cluster of genes P O that are all transcribed as a unit. Promoter Operator • The lac operon in E. coli (a) lac operon is "repressed" contains genes that code for Allolactose (inducer) RNA enzymes that break down the polymerase sugar lactose. P O Promoter Operator • The operon contains (b) lac operon is "induced" regulatory elements: the operator and promoter • Lactose affects a repressor mRNA protein and causes it to fall off the operator, allowing transcription. lac lac Protein 1 Protein 2 Protein 3 TRANSCRIPTIONAL CONTROL IN EUKARYOTES • Gene regulation in eukaryotes is geared toward the whole organism, not the 20 nm individual cell. DNA • Eukaryotic DNA is Core complex packaged around of histones Exterior histone proteins to form histone nucleosomes, which are further packaged into higher-order chromosome structures. • This structure of the chromosomal material (chromatin) affects the availability of DNA for transcription. COMPLEX REGULATION OF GENE EXPRESSION • Gene expression in eukaryotes is controlled in many ways • • • • • • Chromatin structure Initiation of transcription Alternative splicing RNA interference Availability of translational proteins Post-translation modification of protein products DNA tightly packed DNA available for transcription 1. Chromatin structure Access to many genesis affected by the packaging of DNA and by chemically altering the histone proteins. 2. Initiation of transcription Most control of gene expression is achieved by regulating the frequency of transcription initiation. RNA polymerase DNA 3′ Histones Primary RNA transcript 5′ Exon Intron Cut intron 5′ cap 3′ poly-A tail 3. RNA splicing Gene expression can be controlled by altering the rate of splicing in eukaryotes. Alternative splicing can produce multiple mRNAs from one gene. Mature RNA transcript Dicer enzyme RNA hairpins 4. Gene silencing Cell scan silence genes with siRNAs, which are cut from inverted sequences that fold into double-stranded loops. siRNAs bind to mRNAs and block their translation. siRNA Completed polypeptide chain 6. Post-translational modification Phosphorylation or other chemical modifications can alter the activity of a protein after it is produced. 5„ 3„ 5. Protein synthesis Many proteins take part in the translation process, and regulation of the availability of any of them alters the rate of gene expression by speeding or slowing protein synthesis.