1. How are Proteins Made? Coach Fults Chapter 10

2. Decoding the Information in DNA Traits such as eye color, are determined by proteins that are built according to instructions coded in DNA But proteins are not directly built from DNA Ribonucleic Acid is involved

3. Decoding the Information in DNA Like DNA, ribonucleic acid is a nucleic acid- a molecule made of nucleotides linked together RNA differs from DNA in 3 ways 1 st RNA is a single strand 2 nd RNA contains the 5 sugar ribose= it contains 1 more oxygen atoms than deoxyribose 3 rd uracil takes the place of thymine

5. Decoding the Information in DNA A T C G T A  DNA U A G C A U  RNA A gene’s instructions for making proteins are coded in the sequence of nucleotides in the gene The instructions for making a protein are transferred from a gene to a RNA molecule in a process called transcription

6. Decoding the Information in DNA Cells then use 2 different types of RNA to read the instructions on the RNA molecule and put together the amino acids that make up the protein in a process called translation The entire process by which proteins is made from DNA is called gene expression, or protein synthesis

7. Transfer of Info from DNA to RNA The 1 st step to make protein, transcription, takes the info 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

10. Transfer of Info from DNA to RNA 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

11. Transfer of Info from DNA to RNA Step: 2 RNA polymerase then unwinds and separates the 2 strands of double helix, exposing the DNA nucleotides on each strand

12. Transfer of Info from DNA to RNA Step: 3 RNA polymerase adds and then links the complimentary RNA nucleotides as it “reads” the gene. RNA polymerase moves along the nucleotides of DNA strand that has the gene, much like a train moves along a track. Remember that uracil pairs with adenine instead of thymine. RNA eventually hits a “stop” signal.

13. Transfer of Info from DNA to RNA When nucleotides are added in transcription the nucleotides are attached by covalent bonds After the RNA strand is made, the DNA strand binds back by forming hydrogen bonds again

15. Transfer of Info from DNA to RNA Transcription in prokaryotes occurs in the cytoplasm b/c there is no nucleus

16. The Genetic Code: 3-Nucleotide “Words” 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 from of RNA that carries the instructions for making a protein from a gene and delivers it to the site of translation

18. The Genetic Code: 3-Nucleotide “Words” The info is translated from the language of RNA-nucleotides-to the language of proteins- amino acids The RNA instructions are written as a series of 3-nucleotide sequences on the mRNA called codons Each codon along with the mRNA strand corresponds to an amino acid or signifies a start or stop signal for translation

19. The Genetic Code: 3-Nucleotide “Words” In 1961, Marshall Nirenberg deciphered the 1 st codon by making artificial mRNA that contained only the base uracil The mRNA was translated into a protein made up entirely of phenylalanine amino-acid subunits. So he concluded that UUU is the instruction for the amino acid phenylalanine Genetic code- the amino acids and the (start/stop) signals that are coded for by each of the possible 64 mRNA codons

21. RNA’S Role in Translation 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

23. RNA’S Role in Translation Anticodon- is a 3-nucleotide sequence on a tRNA that is complimentary to an mRNA codon. The amino acid that a tRNA molecules corresponds to a particular mRNA codon Ribosomes are composed of both proteins and ribosomal RNA (rRNA) Ribosomal RNA- molecules are RNA molecules that are part of the structure of ribosomes

26. RNA’S Role in Translation A cell’s cytoplasm contains thousand of ribosomes Each ribosome temporarily holds one mRNA and 2 tRNA molecules

28. Translation: Step 1 Translation begins when the mRNA leaves the nucleus and enters the cytoplasm. The mRNA, the 2 ribosomal subunits, and the tRNA carrying the amino acid methionine together from a functional ribosome The mRNA “start” codon AUG, which signals for the beginning of a protein chain, is oriented in a region of the ribosome called the P site, where the tRNA molecule carrying methionine can bind to the start codon

30. Translation: Step 2 The codon in the area of the ribosome called the A site is ready to receive the next tRNA A tRNA molecule with the complimentary anticodon arrives and binds to the codon The tRNA is carrying its specific amino acid

31. Translation: Step 3 Now both the A site and the P site are holding tRNA molecules, each carrying a specific amino acid Enzymes then help form a peptide bond between the adjacent amino acids A peptide bond (amide bond) is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amine group of the other molecule, thereby releasing a molecule of water (H 2 O).chemical bondmoleculescarboxyl groupamine groupwater

32. Translation: Step 4 Afterward, the tRNA in the P site detaches, leaves behind its amino acid, and moves away from the ribosome

34. Translation: Step 5 The tRNA (with its protein chain) in the A site moves over to fill the empty P site. B/c the anticodon remains attached to the codon, the tRNA molecule and mRNA molecule move as a unit. As a result, a new codon is present in the A site, ready to receive the next tRNA and its amino acid An amino acid is carried to the A site by the tRNA and then bonded to the growing protein chain

36. Translation: Step 6 The tRNA in the P site detaches and leaves its amino acid

37. Translation: Step 7 Steps 2-6 are repeated until a “stop” codon is reached. A stop codon is one of 3 (UAG, UAA, or UGA) for which there is no tRNA complimentary anticodon Thus protein synthesis stops, and the protein is released into the cell

39. RNA’S Role in Translation 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

40. RNA’S Role in Translation The genetic code is the same in all organisms For example: (GUC) codes for the amino acid valine in bacteria, eagles, plants, and humans. This is evidence for organisms having a an early common ancestor

41. Protein Synthesis in Prokaryotes Prokaryotic cells typically have ~ 2,000 genes The human genome has ~30,000 Not all genes are transcribed and translated all the time; this would waste energy and materials in the cell Cells can regulate by what is needed

42. Protein Synthesis in Prokaryotes An example of gene regulation that is well understood in prokaryotes is found in the bacterium E. coli. When you eat or drink a dairy product, the disaccharide lactose (“milk sugar”) becomes available to the E. coli living there. E. coli can absorb the material and break it down for energy or for making other compounds

43. Protein Synthesis in Prokaryotes In E. coli, recognizing, consuming, and breaking down lactose into its 2 components, glucose and galactose, requires 3 diff enzymes, each of which is coded for by diff genes

44. Protein Synthesis in Prokaryotes The 3 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 then translates) the 3 genes when lactose is available and turns off the genes when lactose isn’t available

46. Protein Synthesis in Prokaryotes The piece of DNA that overlaps the promoter sites and serves as the on/off switch is called an operator. B/c of its position, the operator is able to control RNA polymerase’s access to the 3 lactose- metabolizing genes

47. Protein Synthesis in Prokaryotes 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. The operon that controls the metabolism of lactose is called the lac operon What determines if the lac operon is on/off? When there is no lactose in the bacterial cell, a repressor turns the operon off.

48. Protein Synthesis in Prokaryotes A repressor is a protein that binds to an operator and physically blocks RNA polymerase from binding to a promoter site 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, letting transcription and translation to occur

50. Protein Synthesis in Eukaryotes These contain much more DNA Constantly turn genes off and on to save energy Operons haven’t been found often in eukaryotic cells. Instead, genes with related function are often scattered on diff chromosomes

51. Protein Synthesis in Eukaryotes: Controlling the Onset of Transcription Most gene regulation in eukaryotes controls the onset of transcription-when RNA polymerase binds to a gene Like prokaryotes, eukaryotes cells use regulatory proteins, but many more proteins are involved in eukaryotes are called transcription factors

53. Protein Synthesis in Eukaryotes: Controlling the Onset of Transcription Transcription factors help arrange RNA polymerases in the correct position on the promoter. A gene can be influenced by many diff transcription factors An enhancer is a sequence of DNA that can be found by a transcription factor. Enhancers typically are located thousands of nucleotide bases away from the promoter. A loop in the DNA may bring the enhancer and its attached transcription factor (called an activator) into contact with the transcription factor and RNA polymerase at the promoter

55. Protein Synthesis in Eukaryotes: Controlling the Onset of Transcription Transcription factors bound to enhancers can activate transcription factors bound to promoters

56. Intervening DNA in Eukaryotic Genes While it is tempting to think of genes are unbroken stretches of nucleotides that code for a protein, this simple arrangement is usually found in prokaryotes In Eukaryotes, many genes are interrupted by introns-long segments of nucleotides that have no coding information Exons- are portions of a gene that are translated (expressed) into proteins

58. Intervening DNA in Eukaryotic Genes 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 mRNA molecule that then is translated

60. Intervening DNA in Eukaryotic Genes Many biologists think this organization of genes adds evolutionary flexibility. Each exon encodes a diff protein By having introns and exons, cells can occasionally shuffle exons between genes and make new genes The thousand of proteins that occur in human cells appear to have arisen as combinations of only a few thousand exons

61. Mutations We already talked about mutations in gametes, but mutations can occur in somatic (body) cells Gene rearrangements- mutations that move an entire gene to a new location This is like you moving to France and can’t speak French Genes sometimes move as part of a transposon (like a flea on a dog) Other times, the portion of the chromosome containing a gene may be rearranged during meiosis

63. Mutations Mutations that change a gene are called gene alterations. These usually result in the placement of the wrong amino acid during protein assembly This can disrupt the protein’s function Point mutation-a single nucleotide changes In a insertion mutation, a sizeable length of DNA is inserted into a gene

67. Mutations Insertions often result when mobile segments of DNA, called transposons, move randomly from one position to another on chromosomes Transposons make up 45% of the human genome In a deletion mutation, segments of a gene are lost, often during meiosis

69. Mutations Because the genetic message is read as a series of triplet nucleotides, insertions and deletions of 1 or 2 nucleotides can upset the triplet groupings Imagine the sentence “THE CAT ATE,” what if the C was missing, it would read “THE ATA TE” A mutation that causes a gene to be read in the wrong 3-nucleotide sequence is called a frameshift mutation