Biology 1403 TTU Chapter 13-15

Dr Reid- TTU BIOL 1403

. LO check: flow chart from gene→protein — what does each arrow represent?

DNA --(transcription)--> pre-mRNA --(processing: 5' cap, splicing, poly-A)--> mature mRNA --(translation)--> polypeptide --(folding/assembly)--> protein

2. Big picture: What is the Central Dogma?

DNA encodes RNA

3. Why do cells transcribe instead of using DNA directly?

To protect the genome and make many temporary working copies (mRNA) for rapid protein production

4. Compare DNA vs RNA: strands

DNA is usually double-stranded

5. Compare DNA vs RNA: sugar

DNA uses deoxyribose

6. Compare DNA vs RNA: bases

DNA: A, T, G, C

7. Where is DNA vs RNA found in eukaryotes?

DNA stays in the nucleus

8. Function differences among RNAs

mRNA carries coding info

9. Define 'gene'

A DNA sequence whose nucleotide order encodes the information to build a functional RNA or protein

10. Given a coding-strand DNA change, how can a protein be unaffected?

If the change is synonymous (degeneracy), occurs outside coding regions, or doesn’t alter key structure/function

11. Given a coding-strand DNA change, how can a protein be shortened?

If a mutation creates a premature stop codon (nonsense) or a frameshift leading to an early stop

12. Label transcription diagram: which strand is template vs coding?

Template is read by RNA Pol to build complementary RNA

13. Label transcription initiation diagram: where are promoter and initiation complex?

Promoter DNA (often with a TATA box) binds basal transcription factors and RNA Pol II to form the pre‑initiation complex

14. Direction check: RNA Pol movement vs RNA synthesis

RNA Pol moves 3'→5' along the template and synthesizes RNA 5'→3'

15. What does 'degenerate code' mean?

Most amino acids are specified by more than one codon

16. Why is degeneracy helpful?

It buffers against some mutations (synonymous or conservative changes)

17. Predict the mRNA from a given template DNA strand

Base pair A↔U, T→A, C↔G

18. From mRNA to protein (high level)

Ribosomes read mRNA codons 5'→3'

19. Purpose of transcription in cells

Make temporary RNA copies (especially mRNA) of DNA instructions so proteins can be produced while DNA stays protected

20. Name the three stages of transcription

Initiation, Elongation, Termination

21. What is a promoter?

A DNA sequence upstream of a gene where transcription factors and RNA Polymerase bind to start transcription

22. Why is the TATA box common in promoters?

A–T pairs have only 2 hydrogen bonds, making local DNA unwinding easier

23. Which eukaryotic RNA polymerase makes most mRNAs?

RNA Polymerase II

24. What do basal transcription factors do?

Assemble at the promoter (e.g., TFIID with TBP), recruit/stabilize RNA Pol II, and form the pre‑initiation complex

25. How do enhancers/silencers differ from the promoter?

They are distal regulatory elements that modulate transcription frequency

26. Which strand is used as the template during transcription?

The template strand is read to synthesize complementary RNA

27. In which direction is RNA synthesized?

5'→3'

28. What chromatin helper allows Pol II to pass nucleosomes?

FACT complex displaces histones ahead of Pol II and redeposits them after

29. How does termination differ among Pol I, II, and III?

Pol I uses specific termination factor/sequence

30. What is pre‑mRNA vs mature mRNA?

Pre‑mRNA contains introns and lacks complete processing

31. What is added at the 5′ end and why?

A 7‑methylguanosine cap

32. What is added at the 3′ end and why?

A poly‑A tail (~200 A’s) after cleavage near AAUAAA

33. Define introns and exons

Introns are intervening sequences removed by splicing

34. What recognizes splice sites and catalyzes splicing?

The spliceosome (proteins + snRNAs) recognizing GU…AG intron boundaries

35. Consequence of a splicing error

Frameshift or exon loss can yield a dysfunctional protein

36. Predict the effect of no 5′ cap

RNA degrades quickly

37. Predict the effect of no poly‑A tail

RNA is less stable

38. Predict the effect of splicing failure

Mature mRNA retains introns → wrong reading frame/early stops → nonfunctional protein

39. What is RNA editing (special case)?

In some systems (e.g., trypanosome mitochondria), guide RNAs direct U‑insertions to fix pre‑mRNA to a functional message

40. How is transcription linked to translation?

Transcription makes mRNA

41. What does it mean that the genetic code is 'degenerate'?

Multiple codons can specify the same amino acid (redundancy)

42. What does AUG do?

It codes for methionine and initiates translation by setting the reading frame

43. Name the three stop codons

UAA, UAG, UGA

44. Ribosome subunits in eukaryotes vs prokaryotes

Eukaryotes: 40S + 60S = 80S

45. Role of tRNA in translation

Adaptor that carries a specific amino acid and base‑pairs via its anticodon with the mRNA codon

46. Name the three ribosomal sites and their functions

A: Aminoacyl (incoming tRNA)

47. What catalyzes peptide bond formation?

rRNA (peptidyl transferase activity) within the large ribosomal subunit (the ribosome is a ribozyme)

48. Energy source for elongation steps

GTP hydrolysis by elongation factors powers tRNA entry and translocation

49. Eukaryotic vs prokaryotic initiation signals

Eukaryotes use the 5′ cap and scan to the first AUG

50. What sets the translation reading frame?

The AUG start codon used for initiation

51. Translate an mRNA to protein (how?)

Start at AUG, read codons 5′→3′, add amino acids until a stop codon

52. From double‑stranded DNA to amino acid sequence (how?)

Use the coding strand as mRNA template (T→U), then translate via the codon table

53. Function of release factors

They recognize stop codons in the A site and trigger hydrolysis to release the completed polypeptide

54. Effect of a nonsense mutation within coding sequence

Introduces an early stop → truncated, usually nonfunctional protein

55. Effect of a frameshift (±1 or 2 nucleotides)

Alters codon grouping → incorrect amino acids downstream and often an early stop

56. Antibiotic examples that inhibit bacterial translation

Tetracycline blocks the A site

57. What is a polysome?

Multiple ribosomes translating one mRNA simultaneously to boost protein output

58. How does a polypeptide become a functional protein?

It folds (± assembles with partners and may undergo modifications) to become functional