1. (genotype, transcription, and translation)
From gene to phenotype
(genotype, transcription, and translation)

2. DNA Form & Function

3. DNA – an ideal genetic material
Faithful replication
Information content
Capable of change

4. DNA Five carbon sugar – deoxyribose Phosphate group One of four bases
Purines
Five carbon sugar – deoxyribose
Phosphate group
One of four bases
Pyrmidines

5. Nucleotide + Nucleotide + Nucleotide + ……
DNA: Polymerization
Nucleotide + Nucleotide + Nucleotide + ……

6. Faithful replication Complementary base pairing and the double helix
Semi-conservative replication

7. DNA replication DNTPs: dATP, dGTP, dTTP, and dCTP
Template DNA (a pre-existing single strand)
DNA polymerase

8. Template DNA (a pre-existing single strand)
DNA replication
Template DNA (a pre-existing single strand)

9. DNA replication DNA Polymerases
Polymerases catalyze the formation of a phosphodiester bond between the 3'-OH of the deoxyribose on the last nucleotide and the 5' phosphate of the dNTP precursor

10. Replication is 5’ to 3’

11. Replication is 5’ to 3’

12. Replication is 5’ to 3’

13. Replication is 5’ to 3’

14. Replication is 5’ to 3’

15. Replication is 5’ to 3’

16. Information content Met Leu Gly Asp Tyr Gly Phe Lys
ATG CTG GGA GAT TAT GGC TTT AAG
AUG CUG GGA GAU UAU GGC UUU AAG

17. Capable of change Replication errors and proofreading
Exonuclease activity - removal of unpaired nucleotide from the 3' end of the chain

18. Mutations result from heritable changes in DNA sequence
May affect transcription, translation, and phenotype
Single nucleotide substitutions can have different consequences on phenotype
Silent
*** CTG GGA GAT TAT GGC TTT AAG***
*** CTG GGA GAT TAT GGC TTC AAG*** alignment
Leu Gly Asp Tyr Gly Phe Lys
Leu Gly Asp Tyr Gly Phe Lys translation
Missense
*** CTG GGA GAT TAT GGC TAT AAG*** alignment
Leu Gly Asp Tyr Gly Tyr Lys translation
Nonsense
*** CTG GGA GAT TAG GGC TTT AAG*** alignment
Leu Gly Asp Tyr Gly Phe Lys
Leu Gly Asp STOP translation

19. DNA Replication - in vivo
Replication begins at an origin - proceeds bi-directionally
In a higher plant chromosome - thousands of origins
The size of the genome
The rate of DNA replication
The length of the S phase  

20. Development of the female gametophyte
Megaspore mother cell (MMC) 
MMC undergoes meiosis
Of 4 megaspores produced 1 survives (most species)
Three post-meiotic mitoses 1 2 3

21. Development of the male gametophyte
The first mitosis gives vegetative and generative nuclei; at the second mitotic division, the generative nucleus gives 2 sperms.
mitosis
mitosis
mitosis
mitosis
mitosis
mitosis
mitosis
mitosis

26. Replication details
Unwinding: The DNA helix opened by helicase enzymes, which break the hydrogen bonds holding the two strands of the helix together. Gyrase facilitates helicase action by relieving tension in coiled DNA.
Stabilization: The unwound DNA is stabilized by a protein (single strand binding protein (SSB)), which speeds up DNA replication.

27. Replication details Priming: Primases form short RNA primers
Synthesis: DNA polymerases use the primer to synthesize the new strand (polymerases cannot start synthesis on their own)
Primer removal: RNA primers removed by exonuclease activity of a polymerase and replaced with DNA

28. Replication details DNA polymerases synthesize new strands 5’ to 3’
The double helix is antiparallel
DNA synthesis is semi-conservative
Therefore DNA synthesis is continuous on the leading strand and
discontinuous on the lagging strand
Multiple priming sites on the lagging strand - Okazaki fragments

36. Replication details
DNA Pol I exonuclease removes RNA Primers in lagging strand
DNA Polymerase adds complementary nucleotides to fill the gaps
DNA Ligase adds phosphate in the remaining gaps of the phosphate - sugar backbone

37. Replication details
Specific polymerases with 3’- 5’ exonuclease activity identify and remove detected mis-matches on the synthesized strand
Proofreading starts at the 3’ end of the synthesized strand and proceeds 3’ - 5’

38. DNA to RNA to protein

39. From gene to phenotype “Central dogma” DNA → RNA → protein DNA
Covered barley:
Lemma and palea adhere
to seed
RNA
Other genes
Pathways
Environmental
signals
Protein

40. Eukaryotic Gene Structure
“DNA sequence specifying a protein”
~200 – 2,000,000 nt (bp)

41. RNA Ribonucleic acid (RNA)
A key nucleic acid in transcription, translation, and regulation
Like DNA except that:
Usually single rather than double stranded
Pentose sugar is ribose rather than deoxyribose
It contains the pyrimidine base uracil (U) rather than thymine (T)
    

42. Classes of RNA Informational (messenger): mRNA - Transcription
Functional (transfer, ribosomal RNA): tRNA, rRNA - Translation
Regulatory (addressed later in the context of gene regulation)

43. Informational (messenger) - mRNA
Single-stranded RNA molecule complementary to one of the DNA strands of a gene
Leaves nucleus; in cytoplasm translated into protein

44. Functional (transfer) - tRNA
Molecules that carry amino acids to the growing polypeptide:
~ 32 different kinds of tRNA in a typical eukaryotic cell
Each the product of a separate gene
~ 80 nucleotides
Double and single stranded regions
Unpaired regions form loops

45. Functional (transfer) - tRNA
Each kind of tRNA carries (at its 3′ end) one of the 20 amino acids 
At one loop, 3 unpaired bases form an anticodon
Base pairing between the anticodon and the complementary codon on a mRNA molecule brings the correct amino acid into the growing polypeptide chain

46. Functional (ribosomal) - rRNA
The ribosome consists of RNA and protein
Site of protein synthesis
Translation of mRNA sequence

47. Transcription
The template strand is also referred to as the antisense (or non-coding)  strand and the non-template strand as the sense (or coding) strand 

48. Transcription
Either strand of the DNA may be the template strand for RNA synthesis for a given gene 

49. Transcription: Initiation
Initiation: Transcription initiated at the promoter
Promoters
Control gene expression: rate, constitutive, inducible
Identify by consensus sequences

50. Transcription: Elongation

51. Transcription: Elongation

52. Transcription: Elongation

53. Transcription: Elongation

54. Transcription: Elongation

55. Transcription: Termination
Specific nucleotide sequence in the DNA signals end of transcription: the “terminator” sequence
The terminator sequences recognized by specific proteins associated with RNA polymerase II
Signal end of transcription and addition of poly-A tail

56. Transcript Processing
Eukaryotes - primary RNA transcript is processed into a mature mRNA before export to the cytoplasm for translation

57. Transcript Processing
5’ cap: 7-methylguanosine added to free phosphate at 5’ mRNA
Prevents degradation and assists in ribosome assembly
3’poly(A tail): After pre-mRNA is cleaved, poly (A) polymerase adds ~200 A nucleotides
Protects against degradation, aids export to cytoplasm, and involved in translation initiation
Splicing: Removal internal portions of the pre-mRNA
Most eukaryotic genes have an intron/exon structure
Splicing removes introns and remaining exons are rejoined

58. Plant Gene Structure

59. The Code
64 codons; 61 represent amino acid codes and 3 cause the termination of protein synthesis (stop codons)
Degeneracy: Most amino acids represented by >1 codon

60. Translation
MDTVAAWPQFEEQDYMTVWPEEQEYRTVWSEPPKRRAGRIKLQETRHPVYRGVRRRGKVGQWVCELRVPVSRGYSRLWLGTFANPEMAARAHDSAALALSGHDACLNFADSAWRMMPVHATGSFRLAPAQEIKDAVAVALEVFQGQHPADACTAEESTTPITSSDLSGLDDEHWIGGMDAGSYYASLAQGMLMEPPAAGGWREDDGEHDDGFNTSASLWSY

61. Translation – Initiation

62. Translation – Elongation

63. Translation – Termination

64. gene            <1..>77
/gene="CBF2A"
mRNA          <1..>772    
/gene="CBF2A"                 
/product="HvCBF2A”
5'UTR          <1..12     
CDS                  
/gene="CBF2A”                 
/note="HvCBF2A-Dt; AP2 domain CBF protein; putative CRT        
binding factor; monocot HvCBF4-subgroup member                  
/codon_start=1                  
/product="HvCBF2A"  
/protein_id="AAX "
/db_xref="GI: "                    
/translation="MDTVAAWPQFEEQDYMTVWPEEQEYRTVWSEPPKRRAGRIKLQE
TRHPVYRGVRRRGKVGQWVCELRVPVSRGYSRLWLGTFANPEMAARAHDSAALALSGH
DACLNFADSAWRMMPVHATGSFRLAPAQEIKDAVAVALEVFQGQHPADACTAEESTTP 
ITSSDLSGLDDEHWIGGMDAGSYYASLAQGMLMEPPAAGGWREDDGEHDDGFNTSASL 
WSY"    
3'UTR          679..>772                    

65. Summary of Transcription and Translation
Sequence
Type
5' atg gac aca tag 3’
Sense (Non-template DNA)
(decode replacing T with U )
3' tac ctg  tgt atc 5'
Anti-sense (Template DNA)
5'aug gac aca uag3'
RNA (decode)
M     D     T           Stop
Amino acid code (See Table)
Methionine, Aspartic acid, Threonine

66. Amino Acid Abbreviations

67. Proteins
Primary, secondary, tertiary, and quaternary structures

68. Structural proteins: economic and health implications
Wheat endosperm storage proteins feed millions and can cause intense suffering in individuals with celiac disease

69. Transcription, Translation, Phenotype
Fragrance in rice