Chapter 17 RQ • Why do dwarf peas fail to make their own gibberellins? • What did the “one gene – one polypeptide” hypothesis used to be called? • What is the “bridge” between DNA and protein synthesis? • What is the process by which one gene is copied into an mRNA strand? • How many mRNA nucleotide bases equal a “codon”?
1. Give early experimental evidence that implicated proteins as the links between genotype and phenotype. • Inherited instructions in DNA direct protein synthesis, thus proteins are the links between genotype and phenotype • Garrod suggested that genes dictate phenotypes through enzymes that catalyze reactions
2. Describe Beadle and Tatum’s experiments with Neurospora, and explain the contribution they made to our understanding of how genes control metabolism. • Relationship between genes and enzymes • Wild type (bread mold) can survive on minimal medium looked for mutants or auxotrophs that could not live because they can’t synthesize molecules • Results one gene – one enzyme hypothesis the function of a gene is to dictate the production of a specific enzyme
One gene – one enzyme Gene codes for a specific enzyme One gene – one polypeptide Most enzymes are proteins Many proteins are not enzymes Proteins that are not enzymes are still gene products Many proteins are comprised of 2 or more polypeptide chains, each chain specified by a different gene 3. Distinguish between “one gene-one enzyme” hypothesis and “one gene-one polypeptide”, and explain why the original hypothesis was changed.
4. Explain how RNA differs from DNA. • Both are nucleic acids; polymers of nucleotides • RNA is different from DNA: - the 5 carbon sugar is ribose not deoxyribose - the nitrogen base is uracil not thymine
Two processes: transcription and translation Transcription the synthesis of RNA using DNA as a template Translation the synthesis of a polypeptide which is directed by mRNA DNA RNA protein 5. Briefly overview, in your own words, how information flows from gene to protein.
Transcription is the synthesis of RNA under the direction of DNA Translation the actual synthesis of a polypeptide, which occurs under the direction of mRNA 6. Distinguish between transcription and translation.
7. Describe where transcription and translation occur in prokaryotes and in eukaryotes; explain why it is significant that in eukaryotes, transcription and translation are separated in space and time. • Prokaryotes lack nuclei so DNA is not segregated from ribosomes or the protein – synthesizing machinery (occurs in rapid succession) • Eukaryotes have nuclear envelopes that segregate transcription in the nucleus from translation in the cytoplasm; mRNA (the intermediary) is modified before it moves from the nucleus to the cytoplasm where translation occurs
8. Define codon, and explain what relationship exists between the linear sequence of codons on mRNA and the linear sequence of amino acids in a polypeptide. • Codon a 3-nucleotide sequence in mRNA that specifies which amino acid will be added to a growing polypeptide or that signals termination the basic unit of the genetic code • Genes are not directly translated into amino acids but are first transcribed as codons into mRNA
9. List the three stop codons and the one start codon. StartAUG StopUAA UAG UGA
10. Explain in what way the genetic code is redundant and unambiguous. • Redundant two or more codons differing only in their 3rd base can code for the same amino acids (UUU & UUC = phenylalanine) • Unambiguous codons code for only ONE amino acid (UUU ONLY codes for phenylalanine)
11. Explain the evolutionary significance of a nearly universal genetic code. • It indicates that the code was established very early in life’s history
12. Explain the process of transcription including the three major steps of initiation, elongation, and termination. Initiation a RNA polymerase attaches at a specific region of DNA called the promoter, and begins transcription (often called the TATA box) Elongation as RNA polymerase moves along the DNA, 10 – 20 bases are exposed at a time for pairing with RNA nucleotides Termination transcription proceeds until RNA polymerase transcribes the termination sequence
13. Describe the general role of RNA polymerase in transcription and explain how it recognizes where to begin. • RNA polymerases bind at the promoter and in eukaryotes they need transcription factors to recognize them • The enzyme separates the 2 DNA strands at the initiation site and transcription begins
14. Specifically, describe the primary functions of RNA polymerase II. • It untwists and opens a short segment of DNA exposing about 10 nucleotide bases one of the exposed DNA strands is the template for base-pairing with RNA nucleotides • It links incoming RNA nucleotides to the 3’ end of the elongating strand, thus, RNA grows one nucleotide at a time in the 5’ to 3’ direction
15. Distinguish among mRNA, tRNA, and rRNA. • mRNA messenger RNA; what the DNA nucleotide sequence is transcribed into • tRNA transfer RNA • rRNA ribosomal RNA; translation occurs on ribosomes, complex particles composed of rRNA and protein that facilitate the orderly linking of amino acids into polypeptide chains
16. Describe the structure of tRNA and explain how the structure is related to the function. • tRNA is transcribed from DNA templates, made in the nucleus and travels out into the cytoplasm • Used repeatedly – picks up its designated amino acid in the cytosol, deposits it at the ribosome, and leaves to pick up another • Consists of a single RNA strand that is only about 80 nucleotides long, has a protruding end which serves as the attachment site for the amino acid
17. Given the sequence of bases in DNA, predict the corresponding codons transcribed on mRNA and the corresponding anticodons of tRNA. DNA CTAGGATGCAAATGC mRNA GAUCCUACGUUUACG tRNA CUAGGAUGCAAAUGC
18. Describe the wobble effect. • It is a relaxation of the base-pairing rules • If one tRNA variety existed for each of the mRNA codons that specifies an amino acid, there would be 61 tRNAs, there are only 45 - this is because some tRNAs can recognize two or more codons
19. Explain how an aminoacyl-tRNA synthetase matches a specific amino acid to its appropriate tRNA; describe the energy source that drives this endergonic process. • There are 20 types of these enzymes in a cell, each specific for an amino acid • The active site of each enzyme fits only a specific combination of amino acid and tRNA • The synthetase catalyzes the covalent attachment of the amino acid to its tRNA in a process driven by the hydrolysis of ATP (which loses 2 phosphates!)
20. Describe the structure of a ribosome and explain how this structure relates to function. • A ribosome is made up of 2 subunits (large and small) – these are constructed of proteins and ribosomal RNA molecules, and are made in the nucleolus • Function is to bring mRNA together with the amino acid-bearing tRNAs, therefore they have binding sites for mRNA and tRNA
21. Describe the process of translation including initiation, elongation, and termination and explain what enzymes, protein factors, and energy sources are needed for each stage. • Initiation when mRNA, tRNA and the first amino acid come together with the ribosome - protein initiation factors bring everything together to begin (GTP provides energy)
Elongation… • Elongation amino acids are added one by one, helped by protein elongation factors 1. Codon recognition – mRNA codon makes a hydrogen bond with the tRNA anticodon (requires GTP hydrolysis) 2. Peptide bond formation – a ribozyme catalyzes the peptide bond creating a polypeptide which then separates from it’s tRNA 3. Translocation – the tRNA moves to another part of the ribosome, and the next codon to be translated steps up; finally the tRNA leaves (requires hydrolysis of GTP)
Termination… • Termination elongation continues until there is a stop codon; a protein release factor binds and adds a water to finish the polypeptide
22. Explain what determines the primary structure of a protein and describe how a polypeptide must be modified before it becomes fully functional. • A gene determines the protein’s primary structure (it’s amino acid sequence) • Primary structure then determines conformation changes • Posttranslational modifications chemical modification by adding sugars, lipids, phosphates, or others
23. Describe what determines whether a ribosome will be free in the cytosol or attached to rough ER. • Free suspended in cytosol and mostly synthesize proteins that dissolve in the cytosol and function there • Bound attached to the cytosol side of the ER and make proteins which are secreted from the cell (ex: insulin) - occurs if the growing polypeptide ITSELF cues the ribosome to attach to the ER – marked by a signal peptide, which targets the protein to the ER
A signal peptide is recognized by the SRP (signal-recognition particle), and this dictates where that particular protein will be headed for work. - as the polypeptide is being synthesized, it begins to snake around to where it will be located within the cell (ER, mitochondria, chloroplast, etc.) 24. Explain how proteins can be targeted for specific sites within the cell.
Prokaryotic A transcription unit can contain several genes, so the resulting mRNA code may code for different, but functionally related, proteins Eukaryotic A transcription unit contains a single gene, so the resulting mRNA codes for synthesis of only one polypeptide 25. Describe the difference between prokaryotic and eukaryotic mRNA.
26. Explain how eukaryotic mRNA is processed before it leaves the nucleus. • In eukaryotes, RNA transcripts are modified before leaving the nucleus to make functional mRNA • This can happen in two ways: 1. Covalent alteration of both the 3’ and 5’ ends 2. Removal of intervening sequences • “Pre-mRNA” is what the molecule is called prior to this alteration
27. Describe some biological functions of introns and gene splicing. • Introns – the noncoding segments of nucleic acid that lie between coding regions • Exons – segments which are eventually expressed through amino acid sequences • Splicing – occurs when the introns are cut out of the initial length to transcribe and translate the portion that will code for used information
28. Explain why base-pair insertions or deletions usually have a greater effect than base-pair substitutions. • Substitutions the replacement of one nucleotide and its partner in the complementary DNA strand with another pair of nucleotides • Insertions and deletions the additions or losses of one or more nucleotide pairs in a gene
29. Describe how mutagenesis can occur. • Mutagenesis the creation of mutations - due to: errors in DNA replication, repair, or recombinations that result in base-pair substitutions, insertions, or deletions The End!