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. Transcription Translation Nuclear envelope Protein Cytoplasm mRNA Nucleus DNA

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′ 5′ 3′ DNA Rewinding U C A 5′ RNA-DNA hybrid helix RNA polymerase mRNA http://www.dnalc.org/resources/3d/12-transcription-basic.html

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 1 2 3 4 5 6 7 3′ poly-A tail 5′ cap Primary RNA transcript Mature mRNA DNA Introns are cut out and coding regions are spliced together Exon (coding region) Intron (noncoding region) Transcription http://www.dnalc.org/resources/3d/rna-splicing.html

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 trial-and-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) Second Letter First Letter Third Letter U C A G U UUU UCU UAU UGU U Phenylalanine Tyrosine Cysteine UUC UCC UAC UGC C Serine UUA UCA UAA Stop UGA Stop A Leucine UUG UCG UAG Stop UGG Tryptophan G C CUU CCU CAU CGU U Histidine CUC CCC CAC CGC C Leucine Proline Arginine CUA CCA CAA CGA A Glutamine CUG CCG CAG CGG G A AUU ACU AAU AGU U Asparagine Serine AUC Isoleucine ACC AAC AGC C Threonine AUA ACA AAA AGA A Lysine Arginine AUG Methionine; Start ACG AAG AGG G G GUU GCU GAU GGU U Aspartate GUC GCC GAC GGC C Valine Alanine Glycine GUA GCA GAA GGA A Glutamate GUG GCG GAG GGG G There are 64 different codons in the genetic code.

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 The large RNA subunit has three binding sites for transfer RNA (tRNA) located directly adjacent to the exposed rRNA sequence on the small subunit. E P A A site mRNA binding site Small subunit Large Large ribosomal P site E site Small ribosomal 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 three-nucleotide 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. 5′ 3′ Amino acid attaches here Anticodon OH

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 U A C 1 2 3 4 The initiating tRNA leaves the ribosome at the E site, and the next tRNA enters at the A site. The initial tRNA occupies the P site on the ribosome. Subsequent tRNAs with bound amino acids first enter the ribosome at the A site. 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. Ribosome Amino acid E site Met tRNA Leu Asn Codon Anticodon P site A site mRNA http://www.dnalc.org/resources/3d/15-translation-basic.html

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. 3′ 5′ tRNA Amino acid mRNA Ribosome Growing polypeptide chain

Gene Expression Gene expression works the same way in all organisms. Key end product Two DNA duplexes mRNA DNA Replication Key starting materials DNA DNA polymerase Ligase Helicase Process Transcription Translation Ribosome RNA polymerase tRNA Polypeptide Amino acids

Gene Expression 5′ 3′ 3 5 mRNA is transported out of the nucleus. In the cytoplasm, ribosomal subunits bind to the mRNA Cap Cytoplasm Completed polypeptide 6 The amino acid chain grows until the polypeptide is completed. Amino acid DNA Introns are excised from the RNA transcript, and the remaining exons are spliced together, producing mRNA. Nuclear pore Small ribosomal subunit mRNA Large membrane 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. 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. Ribosome 4 Ribosome moves toward 3′ end Exons Poly-A tail Primary RNA transcript 1 2 RNA polymerase In the cell nucleus, RNA polymerase transcribes RNA from DNA. Introns 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.

Transcriptional control in prokaryotes An operon is a segment of DNA containing a cluster of genes that are all transcribed as a unit. The lac operon in E. coli contains genes that code for enzymes that break down the sugar lactose. The operon contains regulatory elements: the operator and promoter Lactose affects a repressor protein and causes it to fall off the operator, allowing transcription. Gene 1 Gene 2 Gene 3 Plac O Protein 3 Protein 2 Protein 1 (b) lac operon is "induced" mRNA Operator Promoter (a) lac operon is "repressed" RNA polymerase Repressor Allolactose (inducer)

Transcriptional Control in Eukaryotes 20 nm Core complex of histones Exterior histone DNA Gene regulation in eukaryotes is geared toward the whole organism, not the individual cell. Eukaryotic DNA is packaged around histone proteins to form 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

3 „ 5 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. 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. 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. 2. Initiation of transcription Most control of gene expression is achieved by regulating the frequency of transcription initiation. 1. Chromatin structure Access to many genesis affected by the packaging of DNA and by chemically altering the histone proteins. 6. Post-translational modification Phosphorylation or other chemical modifications can alter the activity of a protein after it is produced. Completed polypeptide chain siRNA Dicer enzyme RNA hairpins Exon Intron Cut intron Mature RNA transcript 5′ cap 3′ poly-A tail RNA polymerase Primary RNA transcript DNA DNA available for transcription Histones DNA tightly packed