How Genes Work Ch. 12

RNA and Protein Synthesis The double helix structure explains how DNA can be replicated but it doesn’t explain how a gene works. Genes are coded DNA instructions that control the production of proteins within a cell. The first step in decoding these genetic messages is to copy part of the nucleotide sequence from DNA to RNA (ribonucleic acid) These RNA molecules will carry out the process of making proteins.

The Structure of RNA Like DNA, RNA consists of a long chain of nucleotides. There are 3 main difference between DNA and RNA: The sugar in RNA is ribose, instead of deoxyribose. RNA is generally single-stranded. RNA contains the base uracil instead of thymine.

Types of RNA In the majority of cells, most RNA molecules are involved in protein synthesis. RNA controls the assembly of amino acids into proteins. There are 3 main types of RNA: messenger RNA (mRNA): RNA molecules that carry copies of the instructions for assembling amino acids into proteins from the DNA to the rest of the cell. ribosomal RNA (rRNA): a form of RNA made up of several dozen proteins. transfer RNA (tRNA): RNA molecules that transfer each amino acid to the ribosome as it is specified by the coded messages in mRNA.

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 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 The path of information is often referred to as the central dogma DNA  RNA  protein 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 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) in place of thymine (T)

Transcription

Gene Expression in Prokaryotes and Eukaryotes 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 non-coding sections of DNA the coding portions are known as exons while the non-coding portions are known as introns

Gene Expression in Prokaryotes and Eukaryotes 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

Processing eukaryotic RNA

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) 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 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

A ribosome is composed of two subunits

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 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

The structure of tRNA.

How translation works

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

Ribosomes guide the translation process

How protein synthesis works in eukaryotes

Transcriptional Control in Eukaryotes 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

DNA coils around histones

Transcriptional Control in Eukaryotes Chromatin structure can be altered in several ways that affect transcription histones can be modified to result in greater condensation of the chromatin this makes promoters less accessible for gene transcription methylation of the DNA can ensure that “turned-off” genes stay off proteins called coactivators can methylate histones and disrupt chromatin coiling, making the DNA more accessible corepressors can remove methyl groups from histones and cause tighter coiling of chromatin and less accessibility to the DNA

Controlling Transcription from a Distance Transcription is much more complex in eukaryotes than in prokaryotes eukaryotic transcription requires proteins called transcription factors basal transcription factors come together to form an initiation complex and recruit RNA polymerase to the promoter specific transcription factors can also bind and will affect the rate at which genes are transcribed

Formation of a eukaryotic initiation complex

Controlling Transcription from a Distance eukaryotic genes have special sequences, called enhancers, which can bind transcription factors called activators even if this regulatory sequence is located far away from the gene it influences, the enhancer can have an effect because the DNA can bend to bring the activator near the RNA polymerase/initiation complex in addition, coactivator and mediator proteins can bind and affect transcription the many factors together form a transcription complex and allow for flexibility in the control of gene expression in eukaryotes

How enhancers work

RNA-Level Control Some controls of gene expression in eukaryotes act after transcription Researchers noted that double-stranded RNA molecules could block the transcription of genes whose sequence was complimentary to that of the double-stranded RNA, called RNA interference or gene silencing.

RNA-Level Control Double-stranded RNA can form when complementary sections of single stranded RNA fold back into hairpin loops In RNA interference an enzyme called dicer cuts double-stranded RNA into smaller bits called siRNA siRNA and proteins form a complex called RISC the siRNA is unwound to be single-stranded and is then able to bind mRNAs complementary to it genes are silenced because the translation of mRNAs is blocked or mRNAs are destroyed

How RNA interference works

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