11/1/2009 Biology 10.2 Review Genes to Proteins 10.2 R EVIEW: Genes to Proteins & Gene Regulation and Structure

11/1/2009 From Genes to Proteins:  Traits, such as eye color, are determined by proteins that are built according to instructions coded in DNA.  Proteins are not built directly from DNA; ribonucleic acid is also involved.  Like DNA, ribonucleic acid is a molecule made of three nucleotides linked together.  When an organism needs to build components of a new cell, a copy of the required DNA part is made.  This copy is called RNA and is almost identical to DNA.

11/1/2009 From Genes to Proteins:  3 differences between DNA and RNA — Unlike the double stranded DNA, RNA is only made up of a single strand. — Furthermore, the base T, thymine, is replaced by U, uracil in RNA. — RNA nucleotides also contain the five-carbon sugar ribose rather than the sugar deoxyribose, which is found in DNA nucleotides.  This RNA string is used by the organism as a template when it builds protein molecules, sometimes called the building blocks of the body.

11/1/2009 From Genes to Proteins:  A gene’s instructions for making a protein are coded in the sequence of nucleotides in the gene.  The instructions for making a protein are transferred from a gene to an RNA molecule in a process called transcription.  The entire process by which proteins are made based on the information encoded in DNA is called gene expression or protein synthesis.  The first step in the making of a protein, transcription, takes the information found in a gene in the DNA and transfers it to a molecule of RNA.  RNA polymerase, an enzyme that adds and links complementary RNA nucleotides during transcription, is required for this process.

11/1/2009 From Genes to Proteins: — As transcription proceeds, the RNA polymerase eventually reaches a “stop signal” in the DNA. — The stop signal is a sequence of bases that marks the end of each gene in eukaryotes, or the end of a set of genes in prokaryotes. — As RNA polymerase moves down the strand, a single strand of RNA grows. — Behind RNA polymerase, the two strands of DNA close up forming hydrogen bonds between complementary bases, reforming the DNA double-helix

11/1/2009 From Genes to Proteins:  Step 1: — Transcription begins when RNA polymerase binds to the gene’s promoter; a specific sequence of DNA that acts as a “start” signal for transcription.  Step 2: — RNA polymerase than unwinds and separates the two strands of the double helix, exposing the DNA nucleotides on each strand.  Step 3: — RNA polymerase adds and than links complementary RNA nucleotides as it “reads” the gene. — RNA polymerase moves along the nucleotides of the DNA strand that has the gene, like a train moves along a track. — Transcription follows the base-pairing rules for DNA replication except that in RNA, uracil, rather than thymine, pairs with adenine.

11/1/2009 From Genes to Proteins: — Like DNA replication, transcription uses DNA nucleotides as a template for making a new molecule. — In DNA replication, the new molecule made is DNA. — In RNA transcription, the new molecule made is RNA instead. — In DNA replication, both strands of DNA serve as templates. — In RNA transcription, only part of one of the strands of DNA (gene) serves as a template.  Transcription in prokaryote cells occurs in the cytoplasm.  Transcription in eukaryote cells occurs in the nucleus, where the DNA is located.  During transcription, many identical RNA molecules are made simultaneously from a single gene.

11/1/2009 From Genes to Proteins:  Different types of RNA are made during transcription, depending on the gene being expressed. When a cell needs a particular protein, it is messenger RNA that is made.  Messenger RNA (mRNA) is a form of RNA that carries the instructions for making a protein from a gene and delivers it to the site of translation.  The information is translated from the language of RNA, nucleotides, to the language of proteins, amino acids.  The RNA instructions are written as a series of three-nucleotide sequences on the mRNA called codons.  Each codon along the mRNA strand corresponds to an amino acid or signifies a start or stop signal for translation.

11/1/2009 In 1961, an American biochemist Marshall Nirenberg, deciphered the first codon by making artificial mRNA that contained only the base uracil. The mRNA was translated into a protein made up entirely of phenylalanine amino-acids subunits. Nirenberg concluded that the codon UUU is the instruction for the amino acid phenylalanine. Later, scientists deciphered the other codons. The complete list of codons, in their groups of threes, makes up the genetic code deciphered by scientists that provides the instructions for all the amino acids and the “start” and “stop” signals that are coded by each of the 64 mRNA possible combinations.

11/1/2009 Translation takes place in the cytoplasm. Here transfer RNA molecules and ribosomes help in the synthesis of proteins. Transfer RNA (tRNA) molecules are single strands of RNA that temporarily carry a specific amino acid on one end. Each tRNA is folded into a compact shape and has an anticodon. An anticodon is a three-nucleotide sequence on a tRNA that is complementary to an mRNA codon.

11/1/2009 R ibosomes are composed of both proteins and ribosomal RNA (rRNA). Ribosomal RNA molecules are RNA molecules that are part of the structure of ribosomes. A cell’s cytoplasm contains thousands of ribosomes. Each ribosome temporarily holds one mRNA and two tRNA molecules. Translation is the process of synthesis of a protein by ribosomes, using mRNA as a template. The genetic message in mRNA is 'read' by organelles called ribosomes in order to make a particular protein. tRNA is also required for this process. tRNAs are specific for one particular amino acid and each tRNA carries required amino acids to the ribosome in order to synthesize the polypeptide chain.

11/1/2009 From Genes to Proteins:  The ribosome 'reads' the mRNA language in the 5' to 3' direction. Each codon (sets of three nucleotide bases) specifies one amino acid from which proteins are made.  So, the mRNA language indicates the sequence of amino acids for the synthesis of a protein. The mRNA language begins with the codon AUG (initiation codon, which starts making a protein chain) and ends with UAA, UAG or UGA (stop codons also called terminators of a protein chain).  As each codon is 'read', the amino acids are carried to the site of formation of the polypeptide chain by the particular tRNA.  Each tRNA has an anticodon that is opposite to the particular codon on the mRNA e.g. if the mRNA codon is AGG then the matching tRNA anticodon is UCC.

11/1/2009 O nce a amino acid is bound to the forming polypeptide chain the next codon is read by the ribosome. The sequence of reading the mRNA and adding an amino acid continues until the 'stop' sequence (codon) is recognized. As the mRNA moves across the ribosome, another ribosome can find the AUG codon on the same mRNA and begin making a second copy of the same protein. In this way many copies of the same protein are made from a single mRNA molecule. With few exceptions, the genetic code is the same in all organisms. For this reason, the genetic code is often described as being nearly universal.

11/1/2009 A lthough prokaryotes, such as bacteria seem human genome; the largest sequenced to date, has about 30,000 genes. Not all genes are transcribed and translated all the time. Cells are able to regulate which genes are expressed and which are not, depending on the needs of the cell. A n example of gene regulation can be found in the bacterium Escherichia Coli. (E. Coli) When you eat or drink a dairy product, the lactose (milk sugar) reaches the intestinal track and becomes available to the E. coli living there. The bacteria can absorb the lactose and break it down for energy or for making other compounds. In E. Coli; recognizing, consuming, and breaking down lactose into it’s parts requires three different types of enzymes, each of which is coded for by a different gene. T he three lactose-metabolizing genes are located next to each other and are controlled by the same promoter site. There is an on-off switch that “turns on” (transcribes and than translates) the three genes when lactose is available and “turns-off” the genes when lactose is not available.

11/1/2009 The piece of DNA that overlaps the promoter site and serves as the on-off switch is called an operator. In bacteria, a group of genes that code for enzymes involved in the same function, their promoter site, and the operator that controls them all function together as an operon. In prokaryotes; gene expression is controlled by these operons. What determines if the lac operon is in the on or off mode? When there is no lactose in the bacterial cell, a repressor turns the operon off. A repressor is a protein that binds to an operator and physically blocks RNA polymerase from binding to a promoter site. This blocking of the RNA polymerase STOPS the transcription of the genes in the operon. The operon that controls the metabolism of lactose in our example is called the lac operon.

11/1/2009 When lactose is present, the lactose binds to the repressor and changes the shape of the repressor. The change in shape causes the repressor to fall off the operator. Now the bacterial cell can begin transcribing the genes that code for the lactose-metabolizing enzymes. By producing the enzymes only when the nutrient is available, the bacterium saves energy. In Summary: In prokaryotes, gene expression is regulated by operons. Gene expression is switched OFF when repressor proteins block RNA polymerase from transcribing a gene.

11/1/2009 E ukaryote cells contain much more DNA than prokaryote cells do. Like prokaryotes cells, eukaryote cells must continually turn certain genes on/off in response to signals from their environment. Operons have NOT been found often in eukaryote cells. Instead, genes with related functions are often scattered on different chromosomes. C ontrolling the Onset of Transcription: Predominantly, gene regulation in eukaryotes controls the onset of transcription. Like prokaryotes, eukaryotes cells use regulatory proteins (proteins to start, stop and regulate the process) These regulatory proteins in eukaryotes are called transcription factors

11/1/2009  Transcription factors help arrange RNA polymerases in the correct position on the promoter. A gene can be influenced by many different transcription factors.  An enhancer is a sequence of DNA that can be bound by a transcription factor.  Enhancers are typically located thousands of nucleotides bases away from the promoter.  A loop in the DNA may bring the enhancer and it’s attached transcription factor (called an activator) into contact with the transcription factors and RNA polymerase at the promoter.  Transcription factors bound to enhancers can activate transcription factors bound to promoters.

11/1/2009  W hile it is tempting to think of a gene as an unbroken stretch of nucleotides that code for a protein, this simple arrangement is usually found only in prokaryotes. — In eukaryotes, many genes are interrupted by introns, long series of nucleotides that have NO coding information. (blank) — Exons are the portions of the genes that are translated (copied or expressed) into proteins. — After a eukaryotic gene is transcribed, the introns in the resulting mRNA are cut out by complex assemblies of RNA and protein called spliceosomes. — The exons that remain are “stitched” back together by the spliceosome to form a smaller RNA molecule that is than translated.

11/1/2009  M any biologists think this organization of genes adds evolutionary flexibility. Each exon encodes a different part of a protein.  By having introns and exons, cells can occasionally shuffle exons between genes and make new genes.  T he thousands of proteins that occur in human cells appear to have arisen as combinations of only a few thousand exons.  Some genes in your cells exist in multiple copies, in clusters of as few as three or as many as several hundred.

11/1/2009  A lthough changes in an organisms hereditary information are rare, they can occur. A change in the DNA of a gene is called a mutation. — M utations in gametes can be passed on to offspring of he affected individual, but mutations in body cells affect only the individual in which they occur. — M utations that move an entire gene to a new location are called gene rearrangements.  M utations that change a gene are called gene alterations. — Gene alterations usually result in the placement of the wrong amino acid during protein assembly. This error will usually disrupt a proteins function.  In a point mutation, a single nucleotide changes.  I n an insertion mutation, a sizable length of DNA is inserted into the gene. — Insertions often result when mobile segments of DNA, called transposons, move randomly from one position to another on chromosomes. — Transposons make up 45 percent of the human genome.  In a deletion mutation, segments of a gene are lost, often during meiosis.

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