Chapter 9 From DNA to Protein

9.1 The Aptly Acronymed RIPs A tiny amount of ricin, a natural protein found in castor-oil seeds, can kill an adult human – there is no antidote Ricin is a ribosome-inactivating protein (RIP) – it inactivates the organelles which assemble amino acids into proteins Other RIPs include shiga toxin, made by Shigella dysenteriae bacteria, and enterotoxins made by E. coli bacteria, including the strain O157:H7

Some RIPs Figure 9.1 A few ribosome-inactivating proteins. The structure of RIPs are strikingly similar. One of their polypeptide chains (red) helps the molecule cross a cell’s plasma membrane. The other chain (orange) destroys the cell’s capacity for protein synthesis.

9.2 DNA, RNA, and Gene Expression Transcription converts information in a gene to RNA DNA → transcription → mRNA Translation converts information in an mRNA to protein mRNA → translation → protein

The Nature of Genetic Information Each DNA strand consists of a chain of four kinds of nucleotides: adenine (A), thymine (T), guanine (G), and cytosine (C) The sequence of the bases in the strand is the genetic code All of a cell’s RNA and protein products are encoded by DNA sequences called genes

Converting a Gene to an RNA Transcription Enzymes use the nucleotide sequence of a gene to synthesize a complementary strand of RNA DNA is transcribed to RNA Most RNA is single stranded RNA uses uracil in place of thymine RNA uses ribose in place of deoxyribose

A DNA Nucleotide base (guanine) 3 phosphate groups sugar (deoxyribose) Figure 9.2 Comparing nucleotides of DNA and RNA. sugar (deoxyribose) A DNA nucleotide: guanine (G), or deoxyguanosine triphosphate

An RNA Nucleotide base (guanine) 3 phosphate groups sugar (ribose) Figure 9.2 Comparing nucleotides of DNA and RNA. sugar (ribose) An RNA nucleotide: guanine (G), or guanosine triphosphate

ANIMATED FIGURE: Gene transcription details To play movie you must be in Slide Show Mode PC Users: Please wait for content to load, then click to play Mac Users: CLICK HERE

deoxyribonucleic acid RNA ribonucleic acid adenine A adenine A DNA deoxyribonucleic acid RNA ribonucleic acid adenine A adenine A sugar– phosphate backbone guanine G guanine G cytosine C cytosine C nucleotide base Figure 9.3 DNA and RNA compared. base pair thymine T uracil U DNA has one function: It permanently stores a cell’s genetic information, which is passed to offspring. RNAs have various functions. Some serve as disposable copies of DNA’s genetic message; others are catalytic. Still others have roles in gene control. Nucleotide bases of DNA Nucleotide bases of DNA Figure 9-3 p151

RNA in Protein Synthesis Messenger RNA (mRNA) Contains information transcribed from DNA Ribosomal RNA (rRNA) Main component of ribosomes, where polypeptide chains are built Transfer RNA (tRNA) Delivers amino acids to ribosomes

Converting mRNA to Protein Translation The information carried by mRNA is decoded into a sequence of amino acids, resulting in a polypeptide chain that folds into a protein mRNA is translated to protein rRNA and tRNA translate the sequence of base triplets in mRNA into a sequence of amino acids

Gene Expression A cell’s DNA sequence (genes) contains all the information needed to make the molecules of life Gene expression A multistep process including transcription and translation, by which genetic information encoded by a gene is converted into a structural or functional part of a cell or body

Take-Home Message: What is the nature of genetic information carried by DNA? Genetic information occurs in DNA sequences (genes) that encode instructions for building RNA or protein products A cell transcribes the nucleotide sequence of a gene into RNA Although RNA is structurally similar to a single strand of DNA, the two types of molecules differ functionally A messenger RNA (mRNA) carries a protein-building code in its nucleotide sequence; rRNAs and tRNAs interact to translate the sequence into a protein

9.3 Transcription: DNA to RNA RNA polymerase assembles RNA by linking RNA nucleotides into a chain, in the order dictated by the base sequence of a gene A new RNA strand is complementary in sequence to the DNA strand from which it was transcribed

DNA Replication and Transcription DNA replication and transcription both synthesize new molecules by base-pairing In transcription, a strand of mRNA is assembled on a DNA template using RNA nucleotides Uracil (U) nucleotides pair with A nucleotides RNA polymerase adds nucleotides to the transcript

The Process of Transcription RNA polymerase and regulatory proteins attach to a promoter (a specific binding site in DNA close to the start of a gene) RNA polymerase moves over the gene in a 5' to 3' direction, unwinds the DNA helix, reads the base sequence, and joins free RNA nucleotides into a complementary strand of mRNA

RNA polymerase binds to a promoter in the DNA RNA polymerase binds to a promoter in the DNA. The binding positions the polymerase near a gene. In most cases, the base sequence of the gene occurs on only one of the two DNA strands. Only the DNA strand complementary to the gene sequence will be translated into RNA. promoter sequence in DNA gene region RNA polymerase 1 2 The polymerase begins to move along the DNA and unwind it. As it does, it links RNA nucleotides into a strand of RNA in the order specified by the base sequence of the DNA. The DNA winds up again after the polymerase passes. The structure of the “opened” DNA at the transcription site is called a transcription bubble, after its appearance. DNA unwinding DNA winding up RNA 3 Zooming in on the gene region, we can see that RNA polymerase covalently bonds successive nucleotides into an RNA strand. The base sequence of the new RNA strand is complementary to the base sequence of its DNA template strand, so it is an RNA copy of the gene. direction of transcription Figure 9.4 Animated Transcription. By this process, a strand of RNA is assembled from nucleotides according to a template: a gene region in DNA. Figure It Out: After the guanine, what is the next nucleotide that will be added to this growing strand of RNA? Stepped Art Figure 9-4 p152

RNA transcripts DNA molecule Figure 9.5 Typically, many RNA polymerases simultaneously transcribe the same gene, producing a structure often called a “Christmas tree” after its shape. Here, three genes next to one another on the same chromosome are being transcribed. Figure It Out: Are the polymerases transcribing this DNA molecule moving from left to right or from right to left? Figure 9-5 p153

Post-Transcriptional Modifications In eukaryotes, RNA is modified before it leaves the nucleus as a mature mRNA Introns Nucleotide sequences that are removed from a new RNA Exons Sequences that stay in the RNA

Alternative Splicing Alternative splicing Allows one gene to encode different proteins Some exons are removed from RNA and others are spliced together in various combinations After splicing, transcripts are finished with a modified guanine “cap” at the 5' end and a poly-A tail at the 3' end

gene promoter exon intron exon intron exon DNA transcription exon new transcript RNA processing Figure 9.6 Animated Post-transcriptional modification of RNA. Introns are removed and exons spliced together. Messenger RNAs also get a poly-A tail and modified guanine “cap.” exon exon exon 5′ 3′ finished RNA cap poly-A tail Figure 9-6 p153

ANIMATED FIGURE: Pre-mRNA transcript processing To play movie you must be in Slide Show Mode PC Users: Please wait for content to load, then click to play Mac Users: CLICK HERE

Take-Home Message: How is RNA assembled? In transcription, RNA polymerase uses the nucleotide sequence of a gene region in a chromosome as a template to assemble a strand of RNA The new strand of RNA is a copy of the gene from which it was transcribed

9.4 RNA and the Genetic Code Base triplets in an mRNA encode a protein-building message Ribosomal RNA (rRNA) and transfer RNA (tRNA) translate that message into a polypeptide chain

mRNA – The Messenger mRNA carries protein-building information to ribosomes and tRNA for translation Codon A sequence of three mRNA nucleotides that codes for a specific amino acid The order of codons in mRNA determines the order of amino acids in a polypeptide chain

Genetic Code Genetic code Consists of 64 mRNA codons (triplets) Twenty kinds of amino acids are found in proteins Some amino acids can be coded by more than one codon Some codons signal the start or end of a gene AUG (methionine) is a start codon UAA, UAG, and UGA are stop codons

three nucleotide bases. In the large chart, the left column lists a codon’s first base, the top row lists the second, and the right column lists the third. Sixty-one of the triplets encode amino acids; the remaining three are signals that stop translation. The amino acid names that correspond to abbreviations in the chart are listed above. Figure It Out: Which codons specify the amino acid lysine (lys)? Figure 9-7a p154

three nucleotide bases. In the large chart, the left column lists a codon’s first base, the top row lists the second, and the right column lists the third. Sixty-one of the triplets encode amino acids; the remaining three are signals that stop translation. The amino acid names that correspond to abbreviations in the chart are listed above. Figure It Out: Which codons specify the amino acid lysine (lys)? Figure 9-7b p154

From DNA to RNA to Amino Acids a gene region in DNA transcription codon codon codon mRNA Figure 9.8 Example of the correspondence between DNA, RNA, and proteins. A DNA strand is transcribed into mRNA, and the codons of the mRNA specify a chain of amino acids. translation methionine (met) tyrosine (tyr) serine (ser) amino acid sequence

rRNA and tRNA – The Translators tRNAs deliver amino acids to ribosomes tRNA has an anticodon complementary to an mRNA codon, and a binding site for the amino acid specified by that codon Ribosomes, which link amino acids into polypeptide chains, consist of two subunits of rRNA and proteins

amino acid attachment site tRNA Structure anticodon anticodon amino acid attachment site Figure 9.10 tRNA structure.

Translation: Ribosome and tRNA Figure 9.10 tRNA structure.

Take-Home Message: What roles do mRNA, tRNA, and rRNA play during translation? mRNA carries protein-building information; the bases in mRNA are “read” in sets of three during protein synthesis; most base triplets (codons) code for amino acids; the genetic code consists of all sixty-four codons Ribosomes, which consist of two subunits of rRNA and proteins, assemble amino acids into polypeptide chains A tRNA has an anticodon complementary to an mRNA codon, and it has a binding site for the amino acid specified by that codon; transfer RNAs deliver amino acids to ribosomes

ANIMATED FIGURE: Structure of a ribosome To play movie you must be in Slide Show Mode PC Users: Please wait for content to load, then click to play Mac Users: CLICK HERE