1. I. DNA as Genetic Material
Frederick Griffith
Avery, McCarty, MacLeod
Hershey and Chase
Chargaff
Pauling
Wilkins and Franklin
Watson and Crick

2. Watson and Crick determined that there are 2 H bonds between A and T and 3 H bonds between C and G

3. T A C G A T G C A T G C T A C G A T G C +

4. Semi-Conservative Theory of Replication
DNA always replicates in a 5’ to 3’ direction
The 5’ and 3’ must always be inverted next to one another.

6. DNA Replication begins at a special site called the origins of replication.
A specific sequence of nucleotides required in initiate replication.
DNA creates a replication fork that opens at the initiation point and creates a replication bubble.

7. Strand separation is achieved by:
Helicases = enzymes that unwind the parental double helix
Single strand binding proteins = keep the strands apart and stabilize the unwound DNA strand

8. DNA Polymerase = catalyze the synthesis of a new DNA strand
Strand can only grow in a 5’  3’ direction
Nucleoside triphosphate = provides energy to form new bonds (two phosphates are lost = endergonic rex)

9. OKAZAKI FRAGMENTS
Leading Strand = synthesized as a single unit in the 5’  3’ direction towards the replication fork
Lagging Strand = discontinuously synthesized against the overall direction of replication

11. Lagging Strand = produces short segments in order to continue to produce 5’  3’
~ 1000 – 2000 nucleotides long in bacteria
~ nucleotides long in eukaryotes
Fragments are joined together by DNA LIGASE

12. Primer = short RNA segment complementary to the DNA strand that starts DNA replication
* Polymerized by PRIMASE
* One primer is required for the leading strand
* Many primers are required for the lagging strand

13. PROOFREADING:
initial base pairing errors are rare (~1 in 10,000)
base pairing is double checked by DNA polymerase which compares added nucleotides against its template
*errors are removed and replaced

14. Genes to Proteins:
Garrod= proposes relationship between genes and proteins
Beadle and Ephrussi= studied the link between eye color and enzyme production in Drosophila
Beadle and Tatum= demonstrated link between genes in enzymes in bread mold (Neurospora crassa)

15. Protein Synthesis involves:
Transcription = synthesis of a mRNA strand using the DNA template
Translation = synthesis of a polypeptide under the direction of the mRNA strand

17. RNA Binding and Initiation:
* RNA polymerases bind to DNA at the promoter region
* Most eukaryotes also contain transcription factors = specific instructions for coding the mRNA strand

18. TATA box = a short nucleotide sequence of T’s and A’s right before the promoter region to help the RNA polymerase to recognize the promoter region

19. Elongation of the RNA Strand:
As the RNA polymerase II moves along the DNA strand:
the helix untwists and opens exposing about 10 base pairs at a time
it links to RNA nucleotides at the 3’ end and the RNA strand grows in a 5’ to 3’ direction

21. Termination of Transcription:
* Transcription continues until RNA polymerase reaches a terminator sequence on the DNA
* Acts as a STOP sign for the RNA polymerase transcription

22. TRANSLATION:
tRNA acts as interpreter between two forms of infomation
tRNA aligns the appropriate amino acids to form a new poly-peptide

23. tRNA molecules:
transfer amino acids from the cytoplasm’s amino acid pool to a ribosome
must recognize the correct codons in mRNA
are specific for only one amino acid
have one end attached to a specific amino acid
the other end attaches to an mRNA codon by pairing with its anticodon

24. ANTICODON: a nucleotide triplet in the tRNA that base pairs with a complementary nucleotide triplet codon in mRNA

25. CODONS: a 3 nucleotide sequence in mRNA that specifies which amino acid will be added
*there are 64 codons and 20 amino acids so there is redundancy = two or more codons code for the same amino acid
* There are 45 distinct types of tRNA so each tRNA molecule recognizes 2-3 mRNA codons specifying the same amino acid

27. Since there is redundancy:
WOBBLE = the use of inosine (I) a modified base in the third position (the wobble position)
CCI codes for GGU, GGA, GGC and GGG (which all code for glycine)

28. Aminoacyl-tRNA Synthetase = a type of enzyme that catalyzes the attachment of an amino acid to its tRNA
*each of the 20 amino acids has its own specific aminoacyl-tRAN sythetase
* Requires an endergonic reaction (ATP driven) that attaches an amino acid to its tRNA by:

29. 1. Activation of amino acid by AMP: the synthetase’s active site binds to an amino acid and ATP  the ATP loses two phosphates and attaches to the amino acid as AMP (adenosine monophosphate)
2. Attachment of the amino acid to tRNA: the appropriate tRNA covalently bonds to the amino acid, displacing AMP from the enzyme’s active site

31. RIBOSOMES: coordinate pairing of tRNA anitcodons to mRNA codons
* Have two subunits (small and large) which are separated when not in-volved in protein synthesis
* When protein synthesis begins, a small subunit and a large subunit come together and bind to the mRNA and the tRNA

32. P SITE = holds the tRNA carrying the growing poly-peptide chain
A SITE = holds the next amino acid to be added

33. Initiation: brings together the mRNA, the first amino acid attached to the tRNA, and the two ribosomal units
( functional ribosome)
* Requires one GTP molecule to help stabilize the attachment of the large ribosomal unit

35. ELONGATION: proteins add amino acids one by one to the initial amino acid
Codon Recognition: mRNA codon in A site forms H-bonds with the anticodon of entering tRNA carrying new amino acids (GTP provides the energy)
Peptide Bond Formation: polypeptide transferase catalyzes formation of a peptide bond between polypeptide at P and a new amino acid at A

36. Translocation: the tRNA at P releases from the ribosome and tRNA at A is translocated to P
codon and anticodon remain bonded, so mRNA and tRNA move as a unit bringing the next codon into the A site
mRNA moves through the ribosome only in the 5’ to 3’ direction
GTP provides the energy for each translocation

38. Termination: end point of translation when the stop codon is reached
when the stop codon is reached, ribosomes at the A site binds to a release factor instead of an amino-acyl tRNA synthetase
* Causes the ribosomal subunits to dissociate from the mRNA strand and separate back into small and large subunits

40. Polyribosomes: cluster of ribosomes simultaneously translating an mRNA molecule

41. *Transcription occurs in the nucleus
* Translation occurs in the cytoplasm
* In eukaryotes, the RNA is processed, so that it is not damaged while moving from the nucleus to the cytoplasm.

43. RNA Processing:
5’ Cap: GTP added to 5’ end of mRNA after transcription begins to protect it from hydrolytic enzymes
Poly A Tail: sequence of a 100+ adenine nucleotides added to the 3’ end of the mRNA before it leaves the nucleus to prevent degradation in the cytoplasm

44. RNA Splicing: process of removing introns and joining exons to form complete mRNA strand because
INTRONS: noncoding sequences in DNA that are positioned between exons
EXONS: coding sequences of a gene