1. Nucleic Acids, DNA, RNA and Protein Synthesis
CHM 341
Suroviec Fall 2016

2. I. Nucleotides, Nucleic Acids and Bases
Planar, aromatic, heterocyclic
Purine (2 rings)
Pyrimidine (1 ring)
Adenine (A)
Guanine (G)
Thyamine (T)
Cytosine ( C)
Uracil (U)

3. B. Nucleosides Ribonucleotides sugar = ribose Deoxyriboneculeotide
Sugar = 2´-deoxyribose

4. C. Nucleotides (total molecule)
Have a phosphate on carbon #5
Can have up to 3 phosphates
Monophosphate (NMP)
Diphosphate (NDP)
Triphosphate (NTP)
Where N is any one of the nucleic acids

5. II. Nucleic Acid Structure
Can be found singly
Most often found in a polymer
DNA (or RNA) polymerizes 5´ phosphate to 3´ OH
Makes phosphodiester bond
Polymer of non-identical residues has a property that individual monomers do not.

6. A. Base composition of DNA
1940’s Erwin Chargaff discovered that when measuring the amount of each base A = T and G = C. Lead to Chargaff’s rules.
Maurie Wilkins and Rosalind Franklin made and X-ray that indicated that DNA was helical in nature
Watson and Crick took this data and other material that hinted that DNA stacked to propose that DNA was double stranded.
Put the bases together in such a way so that the complimentary H-bonds were formed and the width of the base pairs would be similar.

7. Characteristics of DNA model
DNA strands run in opposite directions (antiparallel)
Sugar phosphate backbone is found on outside, bases inside and pair up
Each base is H-bonded with a base on the opposite strand with the same number of H-bonds
A complete turn takes 34 Å and has 10 bases per turn
2 helical polynucleotide chains coiled around a central axis (diameter = 20 Å)
DNA strand is quite stiff and will not bend much around the axis

8.  - DNA
Helix is right handed

9. III. Overview of Nucleic Acid Function
Carries genetic info
Directs protein synthesis
Double stranded nature allows for easy replication
DNA replication
W-C model allows each DNA strand to act as template for replication
2 hypothesis for replication came forth:
Conservative: where the parental DNA strand retains both old stands and creates new ds DNA
Semi conservative: where the created DNA has one old strand and one new strand. Shown to be how DNA replicated

10. DNA, RNA & Protein Synthesis
DNA directs its own replication and is also transcribed into RNA. RNA then translates into proteins.
CENTRAL DOGMA of MOLECULAR BIOLOGY
Transcription: transferring into from DNA --> RNA
Translation: transferring info from RNA --> proteins

11. IV. Replication Involves 20+ proteins
Helicases: opens the double strand, splits the strands apart starting at replication fork rich in A-T
SSB: bind to the single strand DNA stablizing it
Primase: adds short stretches of RNA and allows the the DNA polymerase to start.
DNA polymerase I: catalyzes the addition of deoxynucleotides to the chain
DNA Polymerase I & III: add DNA with high fidelity to the newly growing DNA strand.
Ligase: closes up gaps in the DNA

12. DNA polymerase I
DNA polymerase I catalyzes addition of a addition of dNTP to chain
Requires dATP, dGTP, TTp, dCTP and Mg2+
Elongation occurs 5´ to 3´ where 3´ hydroxyl bind to the new deoxyribonucleotide
DNA polymerase is a “template directed enzyme”

13. DNA polymerase III Adds nucleotides to the 3´ end of the chain
New strand reads 5´ to 3´
Needs a primer with free 3´ hydroxyl group to start addition of new DNA
The strand is going to be started with a RNA primer that is later removed and replaced
The incoming dNTP first forms an appropriate base pair and then the DNA polymerase III links the incoming bases together
Binds complementary DNA nucleotides starting at the 3´ end of the RNA primer at a rate of 1000/second
Makes a mistake 1/108

14. IV. Replication Opening of the DNA
Double stranded DNA is opened by helicase
Kept open by SSB
Exposed DNA bind DNA polymerase III and RNA synthesizing protein primase
This makes the replication fork

15. IV. Replication
Leading strand synthesis begins with synthesis of primase of short RNA primer
dNTPs are added by DNA polymerase III
Continously added to this strand toward the fork

16. Replication Lagging strand synthesis is done in short bursts
Needs multiple RNA primers
Synthesized in opposite direction of the fork
DNA primase moves 5’ to 3’ and makes RNA primer to which DNA is then added by DNA polymerase III

17. Replication
Keeping the DNA sequence correct is important: 1 mispair per 109 base pairs
Polymerase reaction occurs in 2 stages
Incoming dNTP base pairs with the template while enzyme is open catalytically inactive
Polymerization only occurs after polymerase has closed around base pair which positions residues

18. Transcription DNA is in the nucleus
Protein synthesis takes place in the ribosome
RNA is the intermediate
Cells contain 3 types of RNA
Ribosomal RNA (rRNA)
Transfer RNA (tRNA)
Messenger RNA (mRNA)

19. RNA polymerase
RNAP couples together the ribonucleotide triphosphates on DNA templates
Builds RNA in the 5’
3’ direction (reads the DNA in the 3’ --> 5’ direction)

20. RNA polymerase 3’ hydroxyl group attacks the triphosphate
Creates phosphodiester bond
Releases PPi
Does not need a primer

21. RNA polymerase Initiation of RNA synthesis occurs only at promoters
Usually starts at GTP or ATP
New RNA strand base pairs temporarily with DNA template to form DNA/RNA template
DNA must unwind then rewind
Template strand
Nontemplate strand or coding strand

22. RNA polymerase RNA polymerase lacks ability to proof read
No 3’--> 5’ exonuclease activity
One error in 104 ribonucleotides added

23. Post transcription of RNA
In Eukaryotes RNA is further modified
mRNA undergoes gene splicing where introns are removed and exons are rejoined
5’ obtains a cap
3’ gets polyA tail

24. Characteristics of RNA
Seven roles of RNA
mRNA – carries DNA code to make proteins
rRNA – forms complex of 2/3 RNA, 1/3 protein to form protein in ribosome
tRNA – carries the amino acids to the mRNA
snRNA – helps splice exons
Ribozymes – RNA capable of catalytic activity
Antisense RNA – act to bind RNA to stop translation
Viral RNA – carry hereditary information
Contains AUGC
Uracil is less “energy expensive”
Normally single stranded
Has –OH on 2’ carbon of ribose

25. Translation mRNA to proteins mRNA is produced from DNA
Need mRNA, ribosome and tRNA
mRNA is produced from DNA
mRNA read from ribosomes and tRNA

26. Ribosome Large protein/RNA complex 2 units (large/small)
Synthesis begins at start codon near 5’ end
Smaller unit (usually has tRNA bound) binds to AUG codon on mRNA
binds to large subunit
Large unit then binds
Large unit has 3 tRNA binding sites (APE)
A: aminoacyl-tRNA
P:peptidyl-tRNA
E: free-tRNA

27. Initiation AUG signals the beginning of polypeptide chains
Read the code off of the mRNA and translate into amino acids
One start codon
3 stop codon

28. tRNA
Read the code on the mRNA and translate into the correct amino acid
Acceptor stem
5’ terminal nucleotide and 3’ terminal nucleotide (-OH group where amino acid binds)
3’end always has CCA sequence
Specific linkage is catalyzed by amino acyl-tRNA synthetase (tranferase).
Anticodon recognizes the complementary codon on the mRNA

29. Aminoacylation Process of adding an aminoacyl group to a compound
Produces tRNA molecules with their CCA 3’ ends covalently linked to an amino acid
Aminoacyl tRNA synthetase (one specific for each amino acid)
Needs ATP to drive the reaction

30. Initiation and Elongation
mRNA bearing the code for the polypeptide binds to the small ribosome unit
Aminoacyl-tRNA then binds followed by larger ribosomal unit
Aminoacyl-tRNA base-pairs with mRNA codon AUG to start the polypeptide
Chain is elongated by addition of amino acids
Added by individual tRNA
Polypeptides are grown from amino-terminal end to carboxyl-end

31. Elongation mRNA passes through ribosome AUG is held in P site
2nd amino acid binds in the A site
Make peptide bond
Ribosome then moves toward 3’ end using GTP and leaving A site open