IB Biology Review

1. IB Biology Review DNA Transcription and Translation

2. What is Transcription? • The synthesis of mRNA from a DNA template • When the DNA nucleotides are copied into segments of RNA • Transcription occurs when a protein is needed by the body • The “blueprint” for the protein is copied from DNA

3. Transcription Vocab. • Template Strand/Anti-sense Strand/Non-Coding Strand. The DNA strand that is a template for mRNA complementary base pairing during transcription • Non-template Strand/Sense Strand/Coding Strand: The DNA strand that is complementary to the template DNA strand during transcription  • Promoter Region: The region of DNA (a specific sequence of nucleotides) to which RNA polymerase binds to start transcription. (it signals the RNA polymerase where to begin translation along the DNA molecule) • Terminator Region: The region of DNA that signals RNA polymerase to end transcription • RNA processing: Removing the introns in pre-mRNA to produce mature mRNA that is ready for translation • DNA Triplet: Three (3) DNA nucleotides such as ATA or GAC • mRNA Codon: Three mRNA nucleotides such as UAU or CUG that were transcribed from the DNA triplet. Codons form the basis of protein translation because they code for specific amino acids that form proteins

4. What is Translation? • The synthesis of a polypeptide from the genetic information on a mRNA molecule when it couples with a ribosome. It occurs in 4 steps • When the RNA segment tells the ribosome which amino acids to use to build a protein • Translation turns the DNA code into a protein • RNA is the “blueprint” for the protein • The ribosome follows the RNA’s directions

5. Translation Vocab. • tRNA Anticodon: The molecule that transfers/transports specific amino acids to the ribosome where polypeptides • Polypeptides: These are the precursors of proteins and are the product of Translation. They contain all the amino acids in the proper sequence, but the amino acid chain has not yet folded up into its final shape. After folding, carbohydrates are covalently bonded to the folded proteins in the Rough ER . Then, the molecule become a full-fledged protein and is sent to the Golgi Apparatus. • Golgi Apparatus: This is where the proteins produced in the Rough ER are sorted and shipped mostly as secretory proteins used outside the cell such as insulin. • Ribosomes: This organelle is the site of protein synthesis • Bound ribosomes: Ribosomes attached to the walls of the rough ER. Most extra-cellular proteins which will be exported from the cell by exocytosis are synthesized on these ribosomes • Free ribsomes: Ribosomes that are floating free in the cytoplasm. Most proteins used within the cell (such as the transport proteins in cell membrane) are synthesized on these ribosomes • Polyribosomes: An aggregation of several ribosomes attached to one mRNA molecule. (see Figure 17.22). Polyribosomes speed up the translation of a protein. • Point Mutations: A change in only one base pair of DNA in a gene • Substitutions: The replacement of one nucleotide and its complementary nucleotide with another pair of nucleotides. Sometimes these types of mutations are silent mutations as when GAA mutates to GAG (they both code for glutamic acid. Others, such as the Sickle Cell Anemia Case Study described below, cause a change in one of the amino acids in a polypeptide • Insertions and Deletions. These types of mutations lead to frameshift mutations and always produce proteins that are non-functional

6. What is the difference between DNA and RNA nucleotides? • DNA nucleotides are • Adenine • Thymine • Guanine • Cytosine • RNA nucleotides are • Adeneine • Uracil • Guanine • Cytosine

7. What are the steps of transcription? • 1. RNA polymerase unwinds DNA helix • 2. Transcription starts at promoter region • 3. RNA polymerase starts adding free RNA nucleosidesto template strand of DNA • Transcription goes in a 5’ to 3’ direction

8. What are the steps of transcription? Cont. • 4. RNA polymerase continues to add nucleosides • Nucleosides lose two phosphates as they bind to each other • Become nucleotides • 5. RNA polymerase reaches terminator region • 6. RNA polymerase detaches from template strand • 7. RNA strand, now called mRNA, is released from DNA • 8. DNA double helix rewinds

9. The Three Steps of Transcription • 1. Initiation • RNA polymerase binds to helix • RNA polymerase starts to add RNA nucleotides • 2. Elongation • RNA polymerase continues to add nucleotides • 3. Termination • Transcription finishes • RNA polymerase reaches terminator region • mRNA breaks off • RNA polymerase detaches from helix • Helix rewinds

10. tRNA Anticodon What are the steps of translation? • 1. mRNA binds to a ribosome • Small sub-unit first • Then large sub-unit • mRNA translated in whatdirection? • 5’ to 3’, like always • 2. The first transfer RNA (tRNA) binds its anticodon to the start codon of the mRNA • The start codon is always AUG mRNA Codon

11. Codons and Anticodons • Codon is complementary to the DNA strand • Anticodon has the same sequence of nucleotides as DNA (except thymine is uracil) • 64 different codons code for 20 different amino acids • That means there are 64 anticodons that are attached to 20 different amino acids

12. Codons and Anticodons Sample Problem • The template strand of DNA is • TAC-TTG-CTA-CAG-ATT • What will the mRNA (codon) sequence be? • AUG-AAC-GAU-GUC-UAA • What will the tRNA (anticodon) sequence be? • UAC-UUG-CUA-CAG-AUU • tRNA sequence is the same as the template strand, only with U in place of T

13. HL Only: tRNA Activating Enzymes • each amino acid has a specific tRNA-activating enzyme • called aminoacyl-tRNA synthetase • this enzyme binds the specific/correct amino acid to the correct tRNA • uses ATP for energy

14. HL Only: Ribosome Binding Sites • P site holds the tRNA carrying the growing polypeptide chain • A site holds the tRNA carrying the next amino acid to be added to the chain • Discharged tRNAs leave the ribosome from the E site

15. HL Only: DNA Sense and Antisense Strands • DNA sense strand / coding strand has the same base sequence as is as • mRNA • Except uracil replaces thymine • DNA antisense strand / template strand has the same base sequence as • Strand of DNA that is being transcribed (copied)

16. What are the steps of translation? cont. • 3. Second tRNA binds to ribosome and mRNA • Each tRNA brings a specific amino acid with it • 4. The large subunit moves the mRNA strand down after the second tRNA binds • 5. Amino acid on the first tRNA is bound to the second tRNA by a peptide bond • Process continues until ribosome reaches stop codon • 6. Then polypeptide (protein) is released

17. Genetic Code Table • Be familiar with the genetic code table • Be able to use this to translate a segment of mRNA into a protein

18. Using the Genetic Code Table • The letters refer to the mRNA sequence • What is the amino acid sequence if the mRNA sequence is AUG-UCU-GCC-UUA-UCC-UAC • Sequence is • Start/Met. • Serine • Alanine • Leucine • Serine • Tyrosine

19. HL Only: Free and Bound Ribosomes • Free ribosomes • floating in the cytoplasm • produce proteins that stay inside the cell (intracellular proteins) • Bound ribosomes • on the rough endoplasmic reticulum • produce proteins that go outside the cell (extracellular proteins)

20. mRNA Processing • mRNA must be “processed” to remove what? • Introns What are introns? • Non-coding segments of DNA Why would introns have to be taken out? • You wouldn’t want a protein made from them because they don’t do anything!

21. IB Exam Question 1. A certain gene codes for a polypeptide that is 120 amino acids long. Approximately how many nucleotides long is the mRNA that codes for this polypeptide likely to be?(1 mark) A. 30 B. 40 C. 360 D. 480 • Correct answer: C • Each amino acid has three nucleotides • 120 x 3 = 360

22. IB Exam Question 2. Distinguish between the structure of DNA and RNA. (3 marks) • RNA • ribose • (normally) single stranded • uracil • no double helix • DNA • deoxyribose • double stranded • thymine • double helix

23. IB Exam Question 3. Explain the process of DNA Transcription including the role of the promoter region, RNA polymerase, and the terminator and 5’ to 3’ direction (7) • Transcription is the synthesis of mRNA from a DNA template • It occurs in the 5’ to 3’ direction • It occurs in 3 stages: Initiation, Elongation, and Terminations • In Inititiation, RNA polymerase binds to the promoter region • RNA polymerase unwinds the DNA and begins adding complementary RNA nucleotides to the template strand of DNA • In Elongation, the mRNA molecule lengthens • In termination, the RNA polymerase reaches the terminator region and releases the mRNA molecule

24. IB Exam Question 4. Explain the process of translation.(15 marks) • Translation consists of initiation, elongation, translocation and termination; • the binding of a ribosome to mRNA is called initiation; • the small ribosomal sub-unit attaches to mRNA, followed by the large subunit; • next, the first tRNA binds it’s anticodon to the start codon (AUG) of mRNA • This occurs at the A site of the large ribosomal subunit • each tRNA has an anticodon and the corresponding amino acid attached; • this is accomplished by a tRNA activating enzyme which links the correct amino acid to each tRNA; • next, the first tRNA moves to the P site on the ribosome and a second tRNA binds to A site • This is called translocation, the tRNA moves from the A site to the P Site after it delivers its “payload” amino acid • The amino acid on first tRNA is bonded to amino acid on second tRNA; • this forms a peptide bond between the amino acids • the mRNA is translated in the 5' to 3' direction; • and the polypeptide lengthens (called elongation) • this process continues until the ribosome reaches a stop codon (called termination) • at this point, the polypeptide is released;

25. IB Exam Question 5. Compare DNA transcription with translation.(5 marks) • both in 5' to 3' direction; • both require ATP; • DNA is transcribed and mRNA is translated; • transcription produces RNA and translation produces polypeptides; • transcription occurs in the nucleus (of eukaryotes) and translation occurs in the cytoplasm at the rough ER; • tRNA is needed for translation but not transcription;

26. IB Exam Question 6. What is removed to form mature eukaryotic mRNA? (1 mark) A. RNA primers B. Exons C. RNA polymerases D. Introns • Correct answer: D

27. IB Exam Question 7. Discuss the relationship between one gene and one polypeptide. (1 mark) • This means that each gene codes for one unique polypeptide

28. 8. Describe the consequence of a base substitution mutation with regards to sickle cell anemia. (Total 7 marks) • A mutation is a change in the DNA sequence; • This “mistake” often occurs during DNA replication • This changes the mRNA during transcription; • Which, in turn, can change the amino acid sequence; • A substitution mutation leads to a change to one codon; • In sickle cell anemia, glutamic acid is changed to valine / GAG to GTG; • This changes the shape of hemoglobin • The resulting hemoglobin cannot carry oxygen as well;

29. 9. Describe the Genetic Code. (6 marks) • composed of mRNA base triplets; • These are called codons; • each codes for the addition of an amino acid to a growing polypeptide chain; • the genetic code is degenerate; • this means that more than one codon can code for a particular amino acid; • In other words, there are 64 different codons that code for 20 amino acids • the genetic code is universal; • this means it is the same in almost all organisms;