1. Overview: The Flow of Genetic Information
The information content of DNA is in the form of specific sequences of nucleotides
The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins
Proteins are the links between genotype and phenotype
RNA is the manager
Gene expression, the process by which DNA directs RNA and protein synthesis, includes two stages: transcription(RNA) and translation(protein) 1

2. Evidence from the Study of Metabolic Defects
In 1902, British physician Archibald Garrod first suggested that genes dictate phenotypes through enzymes that catalyze specific chemical reactions
He thought symptoms of an inherited disease reflect an inability to synthesize a certain enzyme
Linking genes to enzymes required understanding that cells synthesize and degrade molecules in a series of steps, a metabolic pathway 2

3. Nutritional Mutants in Neurospora:
George Beadle and Edward Tatum exposed bread mold to X-rays, creating mutants that were unable to survive on minimal media
Using crosses, they and their coworkers identified three classes of arginine-deficient mutants, each lacking a different enzyme necessary for synthesizing arginine
They developed a “one gene–one enzyme” hypothesis, which states that each gene dictates production of a specific enzyme 3

4. Lactose Operon of E. coli:
In the 1950s, Jacob and Monod worked with bacterial mutants to dissect gene control circuits
They and others developed evidence of a short-lived intermediate between a gene and the protein that it coded for
This intermediate was required for protein synthesis
Shown to be an RNA molecule-was named messenger RNA 4

5. Basic Principles of Transcription and Translation
RNA is the bridge and the gatekeeper between genes and the proteins for which they code
Transcription is the synthesis of RNA using coded information in DNA
Transcription produces many classes of RNA
Translation is the synthesis of a polypeptide, using information in one class: messenger RNA
Ribosomes are the sites of translation 5

6. It is far more complicated than this in real life
The “Central Dogma” is the old-fashioned concept that cells are governed by a cellular chain of command: DNA RNA protein
Idea developed in 1960s
It is far more complicated than this in real life 6

7. Overview-steps in gene Expression in Prokaryotes and Eukaryotes
Figure 17.3
Overview-steps in gene
Expression in
Prokaryotes and
Eukaryotes
mRNA = messenger RNA
Nuclear envelope
DNA
TRANSCRIPTION
Pre-mRNA
RNA PROCESSING
mRNA
DNA
TRANSCRIPTION
mRNA
Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information.
Ribosome
TRANSLATION
Ribosome
TRANSLATION
Polypeptide
Polypeptide
(a) Bacterial cell
(b) Eukaryotic cell

8. Figure 17.4
DNA template strand 5
DNA 3 A C C A A A C C G A G T
molecule T G G T T T G G C T C A
Gene 1 5 3
TRANSCRIPTION
Gene 2 U G G U U U G G C U C A
+mRNA 5 3
Codon
TRANSLATION
Figure 17.4 The triplet code.
Protein
Trp
Phe
Gly
Ser
Gene 3
Amino acid
Codons in an mRNA molecule are read by translation machinery in the 5 to 3 direction

9. The Genetic Code is a triplet code
How are the instructions for assembling amino acids into proteins encoded into DNA?
There are 20 amino acids, but there are only four nucleotide bases in DNA
Three nucleotides correspond to an amino acid?
codon 9

10. The Genetic Code is Universal
Figure 17.6 Expression of genes from different species.
(a) Tobacco plant expressing
(b) Pig expressing a jellyfish
a firefly gene
gene

11. The code is redundant!(>1 codon/aa)
Second mRNA base U C A G
UUU
UCU
UAU
UGU U
Phe
Tyr
Cys
UUC
UCC
UAC
UGC C U
Ser
UUA
UCA
UAA Stop
UGA Stop A
Leu
UUG
UCG
UAG Stop
UGG
Trp G
CUU
CCU
CAU
CGU U
His
CUC
CCC
CAC
CGC C C
Leu
Pro
Arg
CUA
CCA
CAA
CGA A
Gln
CUG
CCG
CAG
CGG G
First mRNA base (5 end of codon)
Third mRNA base (3 end of codon)
AUU
ACU
AAU
AGU U
Asn
Ser
AUC
Ile
ACC
AAC
AGC C A
Thr
Figure 17.5 The codon table for mRNA.
AUA
ACA
AAA
AGA A
Lys
Arg
AUG
Met or start
ACG
AAG
AGG G
GUU
GCU
GAU
GGU U
Asp
GUC
GCC
GAC
GGC C G
Val
Ala
Gly
Gly
GUA
GCA
GAA
GGA A
Glu
GUG
GCG
GAG
GGG G
The code is redundant!(>1 codon/aa)

12. The code is punctuated (start and stop)
Second mRNA base U C A G
UUU
UCU
UAU
UGU U
Phe
Tyr
Cys
UUC
UCC
UAC
UGC C U
Ser
UUA
UCA
UAA Stop
UGA Stop A
Leu
UUG
UCG
UAG Stop
UGG
Trp G
CUU
CCU
CAU
CGU U
His
CUC
CCC
CAC
CGC C C
Leu
Pro
Arg
CUA
CCA
CAA
CGA A
Gln
CUG
CCG
CAG
CGG G
First mRNA base (5 end of codon)
Third mRNA base (3 end of codon)
AUU
ACU
AAU
AGU U
Asn
Ser
AUC
Ile
ACC
AAC
AGC C A
Thr
Figure 17.5 The codon table for mRNA.
AUA
ACA
AAA
AGA A
Lys
Arg
AUG
Met or start
ACG
AAG
AGG G
GUU
GCU
GAU
GGU U
Asp
GUC
GCC
GAC
GGC C G
Val
Ala
Gly
Gly
GUA
GCA
GAA
GGA A
Glu
GUG
GCG
GAG
GGG G
The code is punctuated (start and stop)

13. 4 Important Characteristics of the Genetic Code
Triplet: 5’ to 3’ in mRNA
Universal
Punctuated
Redundant 13

14. Molecular Components of Transcription
RNA synthesis is catalyzed by RNA polymerase, which separates the DNA strands apart and links together the RNA nucleotides (condensation reaction)
The RNA is complementary to the DNA template strand
RNA synthesis follows the same base-pairing rules as DNA, except that uracil substitutes for thymine 14

15. Nontemplate strand of DNA
RNA nucleotides
RNA polymerase T C C A A A 3 T 5 U C T 3
end T G U A G A C A U C C A C C A 5 A 3 T
Figure 17.9 Transcription elongation. A G G T T 5
Direction of transcription
Template strand of DNA
Newly made RNA

16. Nontemplate strand of DNA 5 3 3 5 Template strand of DNA
Figure
Promoter
Transcription unit 5 3 3 5
DNA
Start point
RNA polymerase 1
Initiation
Nontemplate strand of DNA 5 3 3 5
Template strand of DNA
RNA transcript
Unwound DNA 2
Elongation
Rewound DNA 5 3 3 3 5 5
Figure 17.7 The stages of transcription: initiation, elongation, and termination.
RNA transcript 3
Termination 5 3 3 5 5 3
Completed RNA transcript
Direction of transcription (“downstream”)

17. Eukaryotic complexities
Nucleus has 3 types of RNA polymerase: (Rpol I, Rpol II, R pol III)
All 3 need a lot of help to initiate RNA synthesis
Eukaryotic control signals are very complicated

18. Transcription factors
Promoter
Nontemplate strand
DNA 5′ T A T A A A A 3′ 1
A eukaryotic
promoter 3′ A T A T T T T 5′
TATA box
Start point
Template
strand
Transcription
factors 5′ 3′ 2
Several
transcription
factors bind
to DNA. 3′ 5′
RNA polymerase II
Transcription factors
Figure 17.8 The initiation of transcription at a eukaryotic promoter 5′ 3′ 3′ 3
Transcription
initiation
complex
forms. 3′ 5′ 5′
RNA transcript
Transcription initiation complex

19. Transcription Terminology
RNA polymerase
Template/non-template
+/- sense
Initiation, Elongation, Termination
Upstream/downstream
Promoter/terminator
Transcription unit
Rpol II (for messenger RNA)
Transcription factor
TATA box

20. Eukaryotes modify RNA after transcription
A newly made RNA is called a primary transcript
When a new RNA molecule is first made it is not RTU
It has to be changed or modified prior to use
Enzymes in the eukaryotic nucleus modify primary transcripts before they are sent to the cytoplasm (RNA processing aka RNA modification)
Pre-RNA, mature RNA

21. RNA molecules are usually modified after transcription
Enzymes catalyze changes to the RNA molecule before it is ready to be used.
Changes or modifications can be at the ends or in the middle.
Changes or modifications can involve a single nucleotide at a time or a group.
Modifications help to control gene expression 21

22. Split Genes and RNA Splicing
Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions
These noncoding regions are called intervening sequences, or introns
The other regions are called exons because they are eventually expressed, usually translated into amino acid sequences
RNA splicing removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence

23. Splicing is the most dramatic modification: Many genes are organized into “expressed” sections or exons separated by “unexpressed” sections or introns 5
Exon Intron
Exon
Intron
Exon 3
Pre-mRNA Codon numbers 5
Cap
Poly-A tail
130
31104
105 146
Introns cut out and exons spliced together
mRNA 5
Cap
Poly-A tail
1146 5
UTR 3
UTR
Figure RNA processing: RNA splicing.
Coding segment
The exons and introns are transcribed into RNA
and then the exons are joined together at the RNA level:
Splicing

24. Diverse splicing mechanisms exist
Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites
The RNAs of the spliceosome also catalyze the splicing reaction

25. Small RNAs Spliceosome 5′ Pre-mRNA Exon 2 Exon 1 Intron Spliceosome
Figure A spliceosome splicing a pre-mRNA
Spliceosome
components
mRNA
Cut-out
intron 5′
Exon 1
Exon 2

26. Ribozymes
Ribozymes are catalytic RNA molecules that function as enzymes and some can splice RNA
The discovery of ribozymes rendered obsolete the belief that all biological catalysts were proteins

27. Three properties of RNA enable it to function as a catalyst
It can form a three-dimensional structure because of its ability to base-pair with itself
Some bases in RNA contain functional groups that may participate in catalysis
RNA may hydrogen-bond with other nucleic acid molecules

28. RNA secondary structure-illustrations
U1 snRNA and snRNP
tRNA

29. The Functional and Evolutionary Importance of Introns
Some introns contain sequences that may regulate gene expression
Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing
This is called alternative RNA splicing
Consequently, the number of different proteins an organism can produce is much greater than its number of genes

30. More then one product from each gene
Adds flexibility

31. Alternate splicing works Because genes and proteins
DNA
Exon 1
Intron
Exon 2
Intron
Exon 3
Transcription
Alternate splicing works
Because genes and proteins
are made of modules
RNA processing
Translation
Exons = gene modules
Domains = protein modules
Domain 3
Figure Correspondence between exons and protein domains.
Domain 2
Domain 1
Polypeptide

32. RNA has more roles and functions than any other component
Ribsosomal RNA (rRNA)
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Catalytic RNA (ribozymes)
Structural RNA
Regulatory RNA
The RNA World Hypothesis
Did the first life forms evolve as RNA-based systems?
Did DNA and protein evolve later?

33. Note Card Question (Review)
Promoter RNA splicing/alternative splicing Intron/exon RNA secondary structure Ribozyme Protein domain RNA World Hypothesis