1. Chapter 6 How Cells Read the Genome: From DNA to Protein RNA
Transcription
RNA processing
Translation

2. RNA contains Ribose and Uracil
DNA contains Deoxyribose and Thymine
Phosphodiester bonds between RNA and DNA are the same

3. RNA is single stranded, thus it can fold into specific
structures by base-pairing with complementary sequences

5. TRANSCRIPTION: Promoter RNA Polymerase Recognize initiation site
Separation of DNA
Base pairing
Energy requiring process
No primer required
Process begins at specific site within the promoter

6. RNA polymerase:
DNA is transcribed by RNA polymerase
No primer required
Small window is made in DNA approximately 9 bases in length

7. MOVIE

8. RNA polymerase can move in either direction

9. RNA polymerase uses the antisense strand as a template
to produce primary RNA strand

10. Genes can be expressed with different efficiencies

11. RNA polymerase requires a protein complex at
a promoter to initiate RNA synthesis

12. Enhancer binding proteins can act from a distance to
enhance initiation of transcription.

13. RNA Processing:
Prokaryotes: transcription and translation can be
concurrent.
Eukaryotes: Nucleus (RNA synth) and cytoplasm
(Prot synth) are separated.
Primary transcript undergoes several modifications.
5’ cap is added to 5’ nucleotide; m7Gppp (Stability)
String of adenylic acids are added to the 3’ end (Poly
A tail)
Splicing: internal cleavage to excise introns followed
by ligation of coding exons

14. 5’-methyl cap of mRNAs
Once 25 nucleotides are synthesized the 5’
end of the primary transcript is modified.
Used to ID mRNA and protect from degradation.

15. Polycistronic Monocistronic
Organization of Genes differ in prokaryotes and eukaryotes:
Gene: Unit of DNA that contains the info to specificy synthesis of a single polypeptide
Compact, colinear mRNA Diff chromosomes; one mRNA
Prokaryotes
(operon)
Eukaryotes
Trp mRNA 5’ 3’
Proteins
Polycistronic
Monocistronic

17. Eukaryotes: Organization of DNA within a single gene; Exons and introns
Primary transcript
Exon Intron Exon Intron
Primary transcript
Exon Intron Exon Intron
modification
Exon Exon
Splicing
Cap poly A tail
RNA PROCESSING

18. The structure of two human genes

19. RNA splicing
A specific A attacks the 5’ splice site
Upon cleavage the free OH group reacts with
the next exon sequence releasing the intron

20. The primary transcript can be spliced into several distinct mRNAs
Alternative splicing
The primary transcript can be spliced into
several distinct mRNAs

21. Spliced and polyA mRNA is exported through the nuclear pore

22. TRANSLATION The three roles of RNA in protein synthesis
messenger RNA (mRNA). This will later be translated into a polypeptide.
(Carries information in the form of a three-base code)
transfer RNA (tRNA). RNA molecules that carry amino acids to the growing
polypeptide. (Is key to deciphering the code)
ribosomal RNA (rRNA). This will be used in the building of ribosomes:
machinery for synthesizing proteins by translating mRNA.
(physically move along the mRNA molecule, catalyze assembly of a.a. into prot.

23. Genetic information is carried as three base genetic code
Four bases (A G C T/U) must encode for 20 a.a.
Therefore a combination is required: 43 = 64
Triplet code is called a CODON that must begin at a precise site
Of 64, 61 specify individual a.a.; and three are STOP codons
starting codon is AUG (methionine)
Code is universal, synonymous, degenerate
Reading frame
3rd base in codon “wobble”
frameshifts/deletions/insertions
(MUTATIONS)

24. The genetic code

25. Three different reading frames

26. The decoding function and process:
(tRNA and aminoacyl tRNA synthases) 3D structure important for function
The acceptor stem includes the 5' and 3' ends of the tRNA. The 5' end is generated by RNase P. The 3' end is the site which is charged with amino acids for translation. Some aminoacyl tRNA synthetases interact with both the acceptor 3' end and the anticodon when charging tRNAs.
Each tRNA is recognized by only one synthase; tRNA > a.a. ; tRNA can attach to more than one codon (basis for wobble in genetic code)

27. How do you charge a tRNA with an aa

28. Several different views of a tRNA

29. The wobble position is found at the third base of the codon

30. Polypeptide synthesis is a processive reaction

31. Ribosomes are the protein synthesizing machinery:
Composed of rRNA and more than 50 proteins
Small and large subunit; present in cytosol
Similar 3D structure across species

32. The ribosome is a ribonucleoprotein

33. mRNA Translation Step: MOVIES Basepair to codon, A site
A new peptide is formed
Ejecting spent tRNA and
resetting for next round
MOVIES

34. The Steps of Translation:
1. Initiation: The small subunit of the ribosome binds to a site "upstream“ (on the 5' side) of the start of the message. It proceeds downstream (5' -> 3') until it encounters the start codon AUG. Here it is joined by the large subunit and a special initiator tRNA. The initiator tRNA binds to the P site (shown in pink) on the ribosome. In eukaryotes, initiator tRNA carries methionine (Met). (Bacteria use a modified methionine designated fMet.)
2. Elongation: An aminoacyl-tRNA (a tRNA covalently bound to its amino acid) able to base pair with the next codon on the mRNA arrives at the A site (green) associated with: an elongation factor (called EF-Tu in bacteria) GTP (the source of the needed energy). The preceding amino acid (Met at the start of translation) is covalently linked to the incoming amino acid with a peptide bond (shown in red). The initiator tRNA is released from the P site. The ribosome moves one codon downstream. This shifts the more recently-arrived tRNA, with its attached peptide, to the P site and opens the A site for the arrival of a new aminoacyl-tRNA. This last step is promoted by another protein elongation factor (named EF-G) and the energy of another molecule of GTP.

35. Note: the initiator tRNA is the only member of the tRNA family that can bind directly to the P site. The P site is so-named because, with the exception of initiator tRNA, it binds only to a peptidyl-tRNA molecule; that is, a tRNA with the growing peptide attached.
The A site is so-named because it binds only to the incoming aminoacyl-tRNA; that is the tRNA bringing the next amino acid. So, for example, the tRNA that brings Met into the interior of the polypeptide can bind only to the A site.
3. Termination: The end of the message is marked by one or more STOP codons (UAA, UAG, UGG). No tRNA molecules have anticodons for STOP codons. However, a protein release factor recognizes these codons when they arrive at the A site. Binding of this protein releases the polypeptide from the ribosome. The ribosome splits into its subunits, which can later be reassembled for another round of protein synthesis.
Polysomes
A single mRNA molecule usually has many ribosomes traveling along it, in various stages of synthesizing the polypeptide. This complex is called a polysome.

36. movie

37. DNA to Protein

38. Each step in the synthesis of a protein can ultimately
affect the amount of protein found in a cell