1. Relationship between Genotype and Phenotype
Molecular Basis for
Relationship between Genotype and Phenotype
genotype
DNA
DNA sequence
transcription
RNA
translation
amino acid
sequence
protein
function
phenotype
organism

2. RNA Polymerase
RNA polymerase in E. coli consists of 4 different subunits (see model below).
s recognizes the promoter. Holoenzyme is needed for correct initiation of transcription.
RNA polymerase adds ribonucleotides in 5’ to 3’ direction.
A single type of RNA polymerase transcribes RNA in prokaryotes.

3. Promoter Sequences in E. coli
Refer to Figure 8-7 from Introduction to Genetic Analysis, Griffiths et al., 2015.
Promoters signal transcription in prokaryotes.

4. Transcription Initiation in Prokaryotes
Refer to Figure 8-8 from Introduction to Genetic Analysis, Griffiths et al., 2015.
s subunit positions RNA polymerase for correct initiation.
Upon initiation of transcription, s subunit dissociates.

5. Elongation NTP + (NMP)n (NMP)n+1 + PPi
RNA polymerase adds ribonucleotides in 5’ to 3’ direction.
RNA polymerase catalyzes the following reaction:
DNA
Mg++
RNA polymerase
NTP + (NMP)n
(NMP)n PPi

6. Termination
Termination of transcription occurs beyond the coding sequence of a gene. This region is 3’ untranslated region (3’ UTR), which is recognized by RNA polymerase.

7. RNA polymerase recognizes signals for chain termination.
(1) Intrinsic: Termination site on template DNA consists of GC-rich sequences followed by A’s. Intra-molecular hydrogen bonding causes formation of hairpin loop.
(2) rho factor (hexameric protein) dependent: These termination signals do not produce hairpin loops. rho binds to RNA at rut site. rho pulls RNA away from RNA polymerase.
rut site
In E. coli, this structure signals release of RNA polymerase, thus terminating transcription.

8. Colinearity of Gene and Protein
genotype
DNA
DNA sequence
transcription
RNA
translation
amino acid
sequence
protein
function
phenotype
organism

9. Genetic Code Genetic Code is nonoverlapping.
A codon (three bases or triplet) encodes an amino acid.
Genetic Code is read continuously from a fixed starting point.
There is a start codon (AUG).
There are three stop (termination) codons. They are often called nonsense codons.
Genetic Code is degenerate. Some amino acids are encoded by more than one codon.

10. Relationship between Genotype and Phenotype
Molecular Basis for
Relationship between Genotype and Phenotype
genotype
DNA
DNA sequence
transcription
RNA
translation
amino acid
sequence
protein
function
phenotype
organism

11. * eukaryotic RNA is monocistronic prokaryotic RNA can be polycistronic
Three RNA Polymerases
RNA Polymerase I II
III
Synthesis of
rRNA (except 5S rRNA)
mRNA*, some snRNA
tRNA, some snRNA, 5S rRNA
* eukaryotic RNA is monocistronic
prokaryotic RNA can be polycistronic

12. Eukaryotic RNA
Many proteins must assemble at promoter before transcription.
General transcription factors (GTF’s) bind before RNA polymerase II, while other proteins bind after RNA polymerase II binds.
Primary transcript (pre-mRNA) must be processed into mature mRNA.
1. Cap at 5’ end (7-methylguanosine)
2. Addition of poly(A) tail
3. Splicing of RNA transcript
Chromatin structure affects gene expression (gene transcription) in eukaryotes.

13. Prokaryotic and Eukaryotic Transcription and Translation Compared
Refer to Figure 8-11 from Introduction to Genetic Analysis, Griffiths et al., 2015.