CHAPTER 17 From Gene to Protein GENES SPECIFY

CHAPTER 17 From Gene to Protein

GENES SPECIFY PROTEINS VIA TRANSCRIPTION AND TRANSLATION • Gene expression is the process by which DNA directs the synthesis of proteins (or, in some cases, RNAs). • The one gene-one polypeptide hypothesis states that each gene codes for a polypeptide, which can be-or can constitute part of a protein.

GENES SPECIFY PROTEINS VIA TRANSCRIPTION AND TRANSLATION • Transcription is the synthesis of RNA using DNA as a template. It takes place in the nucleus of eukaryotic cells. • Messenger RNA, or m. RNA is produced during transcription. It carries the genetic message of DNA to the protein-making machinery of the cell in the cytoplasm, the ribosome.

GENES SPECIFY PROTEINS VIA TRANSCRIPTION AND TRANSLATION • In eukaryotes, transcription results in pre-m. RNA, which undergoes RNA processing to yield the final m. RNA. • In prokaryotes, transcription results directly in m. RNA, which is not processed. Transcription and Translation can occur simultaneously.

GENES SPECIFY PROTEINS VIA TRANSCRIPTION AND TRANSLATION • Translation is the production of polypeptide chin using the m. RNA transcript and occurs at the ribosomes. • The instruction for building a polypeptide chin are written as a series of three nucleotide groups: this is called a triplet code.

GENES SPECIFY PROTEINS VIA TRANSCRIPTION AND TRANSLATION • During transcription, only one strand of DNA is transcribed and it is called the template strand. The m. RNA that is produced is said to be complementary to the original DNA strand. The m. RNA base triplets are called codons. • The genetic code is redundant, meaning that more than one codon codes for each of the 20 amino acids. The codons are read based on a consistent reading frame-the groups of three must be read in the correct groupings in order for translation t be successful.

TRANSCRIPTIO N IS THE DNADIRECTED SYNTHESIS OF RNA: A CLOSER LOOK • RNA polymerase is an enzyme that separates the two DNA strands and connects the RNA nucleotides as they basepair along the DNA template strand. • The RNA polymerase can add RNA nucleotides only to the 3’ end of the strand, so RNA elongates in the 5’ to 3’ direction. As RNA nucleotides are added, remember that uracil replaces thymine when base pairing to adenine.

TRANSCRIPTION IS THE DNA-DIRECTED SYNTHESIS OF RNA: A CLOSER LOOK The DNA sequence at which RNA polymerase attaches is called the promoter whereas the DNA sequence that signals the end of transcription is called the terminator. A transcription unit is the entire stretch of DNA that is transcribed into the RNA molecule. A transcription unit may code for a polypeptide or an RNA like transfer RNA or ribosomal RNA.

TRANSCRIPTION IS THE DNADIRECTED SYNTHESIS OF RNA: A CLOSER LOOK • There are three main stages of transcription: 1. Initiation: In bacteria, RNA polymerase recognizes and binds to the promoter. In eukaryotes, RNA polymerase II, the specific RNA polymerase that transcribes RNA, cannot bind to the promoter without supporting help from proteins known as transcription factors. Transcription factors assist the binding of RNA polymerase to the promoter and, thus the initiation of transcription. The whole complex of RNA polymerase II and transcription factors is called a transcription initiation complex.

TRANSCRIPTION IS THE DNADIRECTED SYNTHESIS OF RNA: A CLOSER LOOK 2. Elongation: RNA polymerase moves along the DNA, continuing to untwist the double helix. RNA nucleotides are continually added to the 3’ end of the growing chain. As the complex moves down the DNA strand, the double helix re-forms, with the new RNA molecule straggling away from the DNA template.

Termination: After RNA polymerase transcribes a terminator sequence in the DNA, the RNA transcript is released, and the polymerase detaches. TRANSCRIPTION IS THE DNADIRECTED SYNTHESIS OF RNA: A CLOSER LOOK

EUKARYOTIC CELLS MODIFY RNA AFTER TRANSCRIPTION • In eukaryotes there a couple of key post-transcriptional modifications to RNA-the addition of 5’ cap and the addition of a poly-A tail. • The 5’ cap and the poly-A tail facilitate the export of m. RNA from the nucleus, help protect the m. RNA from degradation by enzymes, and facilitate the attachment of m. RNA to the ribosome.

EUKARYOTIC CELLS MODIFY RNA AFTER TRANSCRIPTION • RNA splicing also takes place in eukaryotic cells. In RNA splicing, large portions of the newly synthesized RNA strand are removed. The sections of m. RNA that are spliced out are called introns and the section that remain and subsequently spliced together by a spliceosome – are called exons.

EUKARYOTIC CELLS MODIFY RNA AFTER TRANSCRIPTION • One amazing thing about spliceosomes work is the role of a special kind of RNA, termed small nuclear RNA (sn. RNA). sn. RNA plays a major role in catalyzing the excision of introns and joining exons. When RNA serves a catalytic role, the molecule is termed ribozyme. For may years it was thought that only proteins could be catalytic, but the discovery of ribozymes totally changed that idea! • Another rethinking that has taken place came with the realization that we have only about 20, 000 genes to make approximately 100, 000 polypeptides. • One gene can often make more than one polypeptide. An intron removed in the production of one polypeptide can be an exon in the second polypeptide made from the same gene! • Alternative RNA splicing allows for different combinations of exons, resulting in more than one polypeptide per gene.

TRANSLATION IS THE RNADIRECTED SYNTHESIS OF A POLYPEPTIDE: A CLOSER LOOK • In addition to m. RNA, two additional types of RNA play important roles in translation: transfer RNA (t. RNA) and ribosomal RNA (r. RNA). • t. RNA functions in transferring amino acids from a pool of amino acids in the cell’s cytoplasm to a ribosome. The ribosome accepts the amino acid from t. RNA and incorporates the amino acid into a growing polypeptide chain.

TRANSLATION IS THE RNADIRECTED SYNTHESIS OF A POLYPEPTIDE: A CLOSER LOOK • Each type of t. RNA is specific for a particular amino acid at one end it loosely binds the amino acid and at the other end it has a nucleotide triplet called the anticodon, which allows it to pair specifically with a complementary codon on the m. RNA.

TRANSLATION IS THE RNADIRECTED SYNTHESIS OF A POLYPEPTIDE: A CLOSER • LOOK A codon is an m. RNA triplet Since there are four different nucleotides (A, T, C, and G), taking them three at a time results in 64 codons. • The m. RNA is read codon by codon and one amino acid is added to the chain for each codon read. • The rules for base pairing between the third base of a codon and the corresponding base of a t. RNA anticodon are not as strict as those for DNA and m. RNA codons. This relaxation of base-pairing rules is called wobble.

TRANSLATION IS THE RNADIRECTED SYNTHESIS OF A POLYPEPTIDE: A CLOSER LOOK • r. RNA complexes with proteins to form the two subunits that form ribosomes. Ribosomes have three binding sites for t. RNA. • A P site which holds the t. RNA that carries the growing polypeptide chain. • An A site, which holds the t. RNA that carries the amino acid that will added t the chain next. • An E site, which is the exit site for t. RNA.

TRANSLATION IS THE RNADIRECTED SYNTHESIS OF A POLYPEPTIDE: A CLOSER • Translation, like transcription can be divided into LOOK three stages: 1. Initiation: A. A small ribosomal subunit binds to m. RNA in such way that the first codon of the m. RNA strand, which is always AUG, is paced in the proper position. B. t. RNA with anticodon UAC, which carries the amino acid methionine, hydrogen bonds to the first codon (initiation factors are proteins that assist in holding all this together). C. Large subunits of ribosome attaches, allowing the t. RNA with methionine to attach to the P site. The A site is now

TRANSLATION IS THE RNADIRECTED SYNTHESIS OF A POLYPEPTIDE: A CLOSER • LOOK Elongation: Also has three steps.

TRANSLATION IS THE RNADIRECTED SYNTHESIS OF A POLYPEPTIDE: A CLOSER LOOK 3. Termination: A stop codon in the m. RNA is reached and translation stops. A protein called release factor binds to the stop codon, ad the polypeptide is freed from the ribosome.

TRANSLATION IS THE RNADIRECTED SYNTHESIS OF A POLYPEPTIDE: A CLOSER LOOK Polypeptides then fold to assume their specific conformation, assume their specific conformation, and they are sometimes modified further to render the functional. The destination of a protein is often determined by the sequence of about 20 amino acids at the leading end of the polypeptide chain. The signal peptide, the sequence of the leading 20 or so amino acids, serve as a sort of cellular zip code, directing proteins to their final destination.

MUTATIONS OF ONE OR A FEW NUCLEOTIDES CAN AFFECT PROTEIN Mutations are alterations in the STRUCTURE AND FUNCTION genetic material of the cell; point mutations are alterations of just one base pair of gene. They come in two types. 1. A nucleotide-pair substitution is the replacement of one nucleotide and its partner with another pair of nucleotides. Missense mutations are those substitutions that enable the codon to still code for the amino acid, although it might not be the correct one.

MUTATIONS OF ONE OR A FEW NUCLEOTIDES CAN AFFECT PROTEIN STRUCTURE AND FUNCTION 2. Insertions and deletions refer to the additions and losses of nucleotide pairs in a gene. If they interfere with the codon groupings, they can cause a frameshift mutation, which causes the m. RNA to be read incorrectly.

MUTATIONS OF ONE OR FEW NUCLEOTIDES CAN AFFECT PROTEIN STRUCTURE AND FUNCTION Mutagens are substances or forces that interact with DNA in ways that cause mutations. X-rays and other forms of radiation are known mutagens, as are certain chemicals.