1. Big Questions How is the structure of DNA related to its function?
How does DNA allow for heritability?
How does DNA allow for traits in an organism?
How do mutations affect DNA structure and function?

2. Central Dogma
"Central Dogma": Term coined by Francis Crick to explain how information flows in cells.

3. Replication
Replication can only begin at specific locations ("origins") on a chromosome
Once it begins, replication proceeds in two directions from the origin
The replication bubble

6. Helicase: Opens the helix (which causes strand separation)
Single Strand Binding Proteins ("SSBP's"): Keep the strand open
Primase: Puts down a small RNA primer which is necessary for DNA polymerase to bind to at the origin.
DNA Polymerase: Enzyme Responsible for DNA synthesis.
Topoisomerase: Rotates the DNA to decrease torque (which would shred the helix.

8. Nucleotides are added to the 3' end of the DNA strand
DNA replication can only occur in the 5' to 3' direction
DNA is "anti-parallel": Both strands have opposite 5' to 3' orientations (one is "upside-down" compared to the other)

9. 2. Elongation
Nucleotides are added to the new strand of DNA in the 5' to 3' direction.
There is an issue: DNA is anti-parallel
As the replication machinery moves along the chromosome, only one strand of DNA (the "leading strand") can be made in a continuous, 5' to 3' piece.

11. The other strand (the "lagging strand") has to be made in smaller, discontinuous 5' to 3' segments ("Okazaki fragments") which are then stitched together by the enzyme ligase

12. Joining
DNA polymerase removes RNA primer and fills with DNA nucleotide
DNA Ligase – links two sections of DNA together

13. Replication Fork

14. 3. Termination Elongation continues until replication bubbles merge
The ends of linear eukaryotic chromosomes pose a unique challenge
Each round of replication shortens the 5' end of the lagging strand (by about bp)
If this continued indefinitely, chromosomes would get shorter and shorter after each replication.
Information would start to be lost

15. Telomeres Ends of eukaryotic chromosomes short, repeating DNA sequence
Vertebrate Telomere: TTAGGG
TELOMERASE - enzyme responsible for replicating the ends of eukaryotic chromosomes
Uses an RNA template to add more telomere sequence during replication

16. Proofreading
There are 5 different DNA polymerases described in prokaryotic cells.
serve a variety of functions
DNA polymerase III- Is responsible for elongation
Rate of elongation is ~500 bases/second in E. coli
The eukaryotic analog DNA polymerase elongates at a rate of ~50 bases/second
The initial error rate is 1 in 10,000
300,000 mutations every time a human cell divided
Proof-reading reduces error rate to 1 in 10 billion (less than 1 per 3 human cell divisions)

17. Transcription

18. 1. Initiation
RNA polymerase attaches to a "promoter" region in front ("upstream") of a gene
Promoters have characteristic DNA sequences (ex "TATA Box" in eukaryotes)

20. 2. Elongation
Similar to DNA replication, RNA production occurs in a 5' to 3' direction.
The template strand of DNA is the one that the RNA transcript is being produced off of (sequence is opposite to the transcript)

22. 3. Termination
Transcript production continues until the end of the transcription unit is reached.

23. Types of RNA Messenger RNA (mRNA): complementary to DNA
C=G, A=U
Travel from nucleus to ribosome
Direct synthesis of protein
Transfer RNA (tRNA): brings amino acids to ribosome
Ribosomal RNA (rRNA): Major structural building block of ribosomes

25. Transcription happens in the nucleus. An RNA copy of a gene is made.
Then the mRNA that has been made moves out of the nucleus into the cytoplasm
Once in the cytoplasm, the mRNA is used to make a protein
Cytoplasm of cell
Nucleus
DNA
mRNA

26. Processing mRNA

27. A modified nucleotide is added to the 5' end of the transcript.
A tail of several hundred adenine residues is put on the 3' end of the transcript.
These modifications function in nuclear export and maintenance of the mRNA

28. Exon Splicing
Eukaryotic genes contain large stretches of non-coding DNA ("introns") interspersed between coding DNA ("exons")
To produce a functional protein, the introns must be removed
the exons must be spliced together prior to the movement of the mRNA transcript to the nucleus
This process is accomplished by a spliceosome

32. Why Introns? Not really answered. Evolutionary baggage? Selfish genes?
We do know that having multiple exons in a gene allows eukaryotes to make multiple functional proteins from one gene ("alternative splicing")

33. Translation
RNA polypeptide

34. 3 base sequence at the bottom – anticodon
Ribosomes
2 subunits – only together during translation
Attaches to mRNA strand
tRNA
3 base sequence at the bottom – anticodon
Matches the codon on mRNA strand

35. The Ribosome The site of protein synthesis All cells have ribosomes
Composed of two subunits
Has three "sites":
A site: "Aminoacyl"- amino acids enter ribosome
P site: "peptidyl"- growing polypeptide is kept
E site: "exit"- empty tRNA molecules leave

37. tRNA
Transfer RNA molecules
Brings amino acids to ribosome

38. Genetic Code Universal across all domains of life three bases = codon
There are 64 possible codons (for 20 possible amino acids).
The code has "start" and "stop“ codons

39. The code was cracked largely by Marshall Nirenberg
Put synthetic RNA into "cell free" E. coli extract and analyzed the polypeptides that were made.
Nobel Prize: 1968

40. 1. Initiation The mRNA attaches to the ribosome
Methionine is brought to the start codon (AUG) by the methionine tRNA

41. tRNA binding at the ribosome
anti-codon matches with the codon

42. The next codon determines the amino acid to be brought
The incoming tRNA enters at the A-site.
4. The next codon is now available in the A-site for the next incoming charged tRNA
3. The ribosome shifts ("Translocates"). The tRNA with the polypeptide is now in the P-site.
The uncharged amino acid is now in the E-site.
2. The growing polypeptide is transfered to the new tRNA molecule. A peptide bond is formed.

43. 3. Termination
When a stop codon (UAG, UAA, or UGA) is encountered, a release factor binds to the A-site.
The polypeptide chain is released.
The ribosome disassembles.

44. The Process of Translation
Figure 8.9

45. The Process of Translation
Figure 8.9

46. The Process of Translation
Figure 8.9

47. The Process of Translation
Figure 8.9

48. The Process of Translation
Figure 8.9

49. The Process of Translation
Figure 8.9

50. The Process of Translation
Figure 8.9

51. The Process of Translation
Figure 8.9

53. Since prokaryotes do not have a nucleus, transcription and translation can be coupled.
Polyribosomes: simultaneous translation of a transcript (even while that transcript is still being made.

55. Replication DNA Helicase unzips DNA RNA Primers bind to DNA strands
DNA Polymerase adds nucleotides to DNA
Leading – continuous adding of bases
Lagging – Okazaki fragments
A-T and C-G
DNA Ligase fills in gaps

56. Transcription Unzip DNA (helicase)
RNA Polymerase binds to synthesize RNA
Match up bases to one strand of DNA
Uracil instead of thymine
mRNA detaches from the DNA
mRNA moves out of nucleus and into cytoplasm

57. Translation mRNA attaches to ribosomes tRNA moves into ribosome
Anticodon matches with mRNA strand and adds an amino acid
tRNA leaves ribosome
Stop codon is reached & amino acid chain (polypeptide) detaches from ribosome
Folds and creates a protein

58. Mutations
It becomes clear how changes in DNA can affect changes in protein structure, and in physiology. There are 2 major types of DNA-level mutations:
Point mutations: One DNA base is replaced by another DNA base.
Frame-shift mutations: DNA bases are inserted or deleted ("in/dels").
Each type of mutation can have different effects, depending on the situation.

60. Point Mutations
Silent - substitution changes a codon to another codon for the same amino acid.
Missense - substitution changes a codon to a codon for a different amino acid
Nonsense- substitution changes a codon to a stop codon

61. Frameshift Insertions – additions of a nucleotide
Shift the codons
Insertions – additions of a nucleotide
Deletion – loss of a nucleotide
Duplication – repeating sequences of codons