Chapter 9 From DNA to Protein

9.1 Ricin, RIP 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) Inactivates the organelles which assemble amino acids into proteins Other RIPs include Shiga toxin, made by Shigella dysenteriae bacteria, and Shiga-like toxin made by E. coli bacteria

RIPs and Their Sources Castor-oil seeds Jequirity beans Camphor tree seeds Ricin Abrin Cinnamomin Figure 9.1 Lethal lineup: a few toxic ribosome-inactivating proteins (RIPs) and their sources. One of the two chains of a toxic RIP (brown) helps the molecule cross a cell’s plasma membrane; the other (gold) is an enzyme that inactivates ribosomes. Shigella dysenteriae Escherichia coli O157:H7 Shiga toxin Shiga-like toxin

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

DNA to RNA Each DNA strand consists of a chain of the four 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

DNA to RNA DNA is transcribed to RNA DNA versus RNA Enzymes synthesize a complementary strand of RNA from the DNA template DNA versus RNA Most RNA is single-stranded RNA uses ribose instead of deoxyribose as its sugar RNA uses uracil instead of thymine

A DNA Nucleotide: Guanine base (guanine) 3 phosphate groups Figure 9.2 Comparing nucleotides of DNA and RNA. A The DNA nucleotide guanine (G), or deoxyguanosine triphosphate, one of the four nucleotides in DNA. The other nucleotides—adenine, uracil, and cytosine—differ only in their component bases (blue). Three of the four bases in RNA nucleotides are identical to the bases in DNA nucleotides. sugar (deoxyribose)

An RNA Nucleotide: Guanine base (guanine) 3 phosphate groups Figure 9.2 Comparing nucleotides of DNA and RNA. B The RNA nucleotide guanine (G), or guanosine triphosphate. The only difference between the DNA and RNA versions of guanine (or adenine, or cytosine) is that RNA has a hydroxyl group (shown in red) at the 2′carbon of the sugar. sugar (ribose)

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 Comparing the structure and function of DNA and RNA. 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

Types and Functions of RNA Messenger RNA (mRNA) Contains the information transcribed from DNA Ribosomal RNA (rRNA) Main component of ribosomes, which build polypeptide chains Transfer RNA (tRNA) Delivers amino acids to ribosomes

RNA to Protein mRNA is translated to protein Translation rRNA and tRNA translate the sequence of base triplets in mRNA into a sequence of amino acids Translation Information carried by mRNA is decoded into a sequence of amino acids Results in a polypeptide chain that folds into a protein

Gene Expression The DNA sequence (genes) contains all the information needed to make the molecules of life Gene expression is a multistep process Includes transcription and then translation Genetic information from the genes is converted into a structural or functional part of a cell or organism

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 both synthesize new molecules by base-pairing Uracil (U) pairs with adenine (A) RNA polymerase adds nucleotides to transcript

Transcription – Base-Pairing

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 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

Transcription – A New Strand of RNA gene region RNA polymerase RNA promoter sequence in DNA DNA winding up DNA unwinding 1 The enzyme RNA polymerase binds to a promoter in the DNA. The binding positions the polymerase near a gene. Only the DNA strand complementary to the gene sequence will be translated into RNA. 2 RNA polymerase begins to move along the gene and unwind the DNA. As it does, it links RNA nucleotides in the order specified by the sequence of the complementary (noncoding) DNA strand. The DNA winds up again after the polymerase passes. 3 Zooming in on the site of transcription, we see that RNA polymerase covalently bonds successive nucleotides into a new strand of RNA. The new RNA is complementary in sequence to the template DNA strand, so it is an RNA copy of the gene. 5' 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? U T A G C A T A C A C direction of transcription C C G T G A U A A G T C U A U U C U A A G C G G G T

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

Alternative Splicing Allows one gene to encode multiple proteins Some exons removed from RNA Other exons spliced together in various combination After splicing, final transcripts are finished Modified guanine ‘cap’ at the 5' end Poly-A tail at the 3' end

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

9.4 RNA and the Genetic Code mRNA carries the information for building proteins to ribosomes and tRNA for translation Protein building information is carried in codons Sequence of three mRNA nucleotides Codes for a specific amino acid Order of codons in mRNA dictates the order of amino acids in the polypeptide chain

The Genetic Code There are 64 codons possible in making up the genetic code 20 kinds of amino acids found in proteins Some amino acids coded by more than one codon Some codons signal the start or end of genes AUG (methionine) is the start codon UAA, UAG, and UGA are stop codons

A Codon Table Figure 9.7 The genetic code second base first base third base U C A G UUU UCU UAU UGU phe tyr cys UUC UCC UAC UGC ser UUA UCA UAA stop UGA leu UGG trp UUG UCG UAG stop CUU CCU CAU CGU his CUC CCC CAC CGC pro arg CUA CCA CAA CGA gln CUG CCG CAG CGG AUU ACU AAU AGU asn AUC ile ACC AAC AGC thr AUA ACA AAA AGA lys AUG met ACG AAG AGG GUU GCU GAU GGU asp GUC GCC GAC GGC val ala gly GUA GCA GAA GGA glu GUG GCG GAG GGG U U C A G C U C A G U Figure 9.7 The genetic code A Codon table. each codon in mRNA is a set of three nucleotide bases. 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; one of those, AUG, both codes for methionine and serves as a signal to start translation. Three codons are signals that stop translation. A C A G G U C A G

The 20 Amino Acids Specified by the Genetic Code ala arg asn asp cys glu gln alanine (A) arginine (R) asparagine (N) aspartic acid (D) cysteine (C) glutamic acid (E) glutamine (Q) gly his ile leu lys met phe glycine (G) histidine (H) isoleucine (I) leucine (L) lysine ( K) methionine (M) phenylalanine ( F) pro ser thr trp tyr val proline (P) serine (S) threonine (T) tryptophan (W) tyrosine (Y) valine (V) Figure 9.7 The genetic code B Names and abbreviations of the 20 naturally occurring amino acids specified by the genetic code (A).

From DNA through RNA to Protein A T G T A C T C A G a gene region in DNA T A C A T G A G T C transcription mRNA A U G U A C U C A G codon codon codon translation Figure 9.8 Example of the correspondence between DNA, RNA, and protein. A gene region in a strand of chromosomal DNA is transcribed into an mRNA, and the codons of the mRNA specify a chain of amino acids—a protein. met tyr ser protein

All Types of RNA Work Together tRNAs deliver amino acids to ribosomes Contains an anticodon complementary to an mRNA codon Contains a binding site for the amino acid coded by the codon rRNA and proteins make up ribosomes Link amino acids into polypeptide chains Two rRNA subunits and proteins make up each ribosome

rRNA – Ribosome Structure Figure 9.19 Ribosome structure. Each intact ribosome consists of a large and a small subunit. The structural protein components of the two subunits are shown in green; the catalytic rRNA components, in brown. large subunit small subunit intact ribosome

tRNA Structure – Tryptophan A C C anticodon trp amino acid attachment site Figure 9.10 tRNA Structure A Icon and model of the tRNA that carries the amino acid tryptophan. Each tRNA’s anticodon is complementary to an mRNA codon. Each also carries the amino acid specified by that codon.

9.5 Translation: RNA to Protein Translation converts genetic information from mRNA into a new polypeptide chain Amino acid order is determined by codon order Occurs in the cytoplasm Occurs in three stages Initiation Elongation Termination

Overview of Translation in a Eukaryotic Cell 1 Transcription ri r bosome subunits 2 RNA transport tRNA Figure 9.11 Overview of translation in a eukaryotic cell. RNAs are transcribed in the nucleus, then transported into the cytoplasm through nuclear pores. Translation begins when ribosomal subunits and tRNA converge on an mRNA in cytoplasm. 3 Convergence of RNAs mRNNA 4 Translation polypeptide

Initiation Initiation complex forms A small ribosomal subunit binds to mRNA The anticodon of initiator tRNA base pairs with the start (AUG) codon of mRNA A large ribosomal subunit joins the small ribosomal subunit

Elongation The ribosome assembles a polypeptide chain as it moves along the mRNA Initiator tRNA carries methionine, the first amino acid of the chain The ribosome joins each amino acid to the polypeptide chain with a peptide bond

Termination When the ribosome encounters a stop codon, polypeptide synthesis ends Release factors bind to the ribosome Enzymes detach the mRNA and polypeptide chain from the ribosome

1 Ribosome subunits and an initiator tRNA converge on an mRNA. A second tRNA binds to the second codon. first amino acid of polypeptide start codon (AUG) initiator tRNA A peptide bond forms between the first two amino acids. peptide bond 2 The first tRNA is released and the ribosome moves to the next codon. A third tRNA binds to the third codon. 3 A peptide bond forms between the second and third amino acids. 4 A peptide bond forms between the third and fourth amino acids. The process repeats until the ribosome encounters a stop codon in the mRNA. 6 The second tRNA is released and the ribosome moves to the next codon. A fourth tRNA binds the fourth codon. 5 Figure 9.12 Animated Translation. Translation begins when ribosomal subunits and an initiator tRNA converge on an mRNA. Then, tRNAs deliver amino acids in the order dictated by successive codons in the mRNA. The ribosome links the amino acids together as it moves along the mRNA, so a polypeptide forms and elongates. Translation ends when the ribosome reaches a stop codon. Stepped Art Figure 9-11 p156

Translation Ribosomal subunits and an initiator tRNA converge on an mRNA. A second tRNA binds to the second codon. start codon (AUG) A peptide bond forms between the second and third amino acids. initiator tRNA first amino acid of polypeptide The second tRNA is released and the ribosome moves to the next codon. A fourth tRNA brings the next amino acid to be added to the polypeptide chain. A peptide bond forms between the first two amino acids. peptide bond stop codon Figure 9.12 Animated Translation. Translation begins when ribosomal subunits and an initiator tRNA converge on an mRNA. Then, tRNAs deliver amino acids in the order dictated by successive codons in the mRNA. The ribosome links the amino acids together as it moves along the mRNA, so a polypeptide forms and elongates. Translation ends when the ribosome reaches a stop codon. The process repeats until the ribosome encounters a stop codon. Then, the new polypeptide is released and the ribosomal subunits separate. The first tRNA is released and the ribosome moves to the next codon. A third tRNA binds to the third codon.

9.6 Mutated Genes and Their Protein Products If the nucleotide sequence of a gene changes, it may result in an altered gene product, with harmful effects Mutations Small-scale changes in the nucleotide sequence of a cell’s DNA that alter the genetic code Relative uncommon events in normal cells

Mutations and Proteins A mutation that changes a UCU codon to UCC is “silent” It has no effect on the gene’s product because both codons specify the same amino acid Other mutations can have severe consequences for the organism May change an amino acid in a protein Can result in a premature stop codon that shortens a protein

Common Mutations Base-pair-substitution Deletion or insertion May result in a premature stop codon or a different amino acid in a protein product Example: sickle-cell anemia Deletion or insertion Can cause the reading frame of mRNA codons to shift, changing the genetic message Example: thalassemia

Examples of Mutations Figure 9.13 Examples of mutations pro glu glu lys ser pro gly arg ser leu A Hemoglobin, an oxygen-binding protein in red blood cells. This protein consists of four polypeptides: two alpha globins (blue) and two beta globins (green). Each globin has a pocket that cradles a heme (red). Oxygen molecules bind to the iron atom at the center of each heme. B Part of the DNA (blue), mRNA (brown), and amino acid sequence of human beta globin. Numbers indicate nucleotide position in the mRNA. D A base-pair deletion shifts the reading frame for the rest of the mRNA, so a completely different protein product forms. The mutation shown results in a defective beta globin. The outcome is beta thalassemia, a genetic disorder in which a person has an abnormally low amount of hemoglobin. Figure 9.13 Examples of mutations pro val glu lys ser C A base-pair substitution replaces a thymine with an adenine. When the altered mRNA is translated, valine replaces glutamic acid as the sixth amino acid. Hemoglobin with this form of beta globin is called HbS, or sickle hemoglobin. pro glu glu glu glu E An insertion of one nucleotide causes the reading frame for the rest of the mRNA to shift. The protein translated from this mRNA is too short and does not assemble correctly into hemoglobin molecules. As in D, the outcome is beta thalassemia.

Points to Ponder Why are ribosomes essential to protein synthesis? Why is transcription necessary? Why don’t cells use their DNA as a direct model for protein synthesis? In what ways does RNA differ from DNA?