overview: the flow of genetic information the information content of dna is in the form of specific...
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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)
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
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
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
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
• 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
Figure 17.3
DNA
mRNARibosome
Polypeptide
TRANSCRIPTION
TRANSLATION
TRANSCRIPTION
TRANSLATION
Polypeptide
Ribosome
DNA
mRNA
Pre-mRNARNA PROCESSING
(a) Bacterial cell (b) Eukaryotic cell
NuclearenvelopeOverview-steps in gene
Expression inProkaryotes andEukaryotesmRNA = messenger RNA
Figure 17.4
DNAtemplatestrand
TRANSCRIPTION
+mRNA
TRANSLATION
Protein
Amino acid
Codon
Trp Phe Gly
5
5
Ser
U U U U U3
3
53
G
G
G G C C
T
C
A
A
AAAAA
T T T T
T
G
G G G
C C C G G
DNAmolecule
Gene 1
Gene 2
Gene 3
C C
Codons in an mRNA molecule are read by translation machinery in the 5 to 3 direction
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
The Genetic Code is Universal
(a) Tobacco plant expressing a firefly gene gene
(b) Pig expressing a jellyfish
Second mRNA base
Fir
st m
RN
A b
ase
(5 e
nd
of
cod
on
)
Th
ird
mR
NA
bas
e (3
en
d o
f co
do
n)
UUU
UUC
UUA
CUU
CUC
CUA
CUG
Phe
Leu
Leu
Ile
UCU
UCC
UCA
UCG
Ser
CCU
CCC
CCA
CCG
UAU
UACTyr
Pro
Thr
UAA Stop
UAG Stop
UGA Stop
UGU
UGCCys
UGG Trp
GC
U
U
C
A
U
U
C
C
CA
U
A
A
A
G
G
His
Gln
Asn
Lys
Asp
CAU CGU
CAC
CAA
CAG
CGC
CGA
CGG
G
AUU
AUC
AUA
ACU
ACC
ACA
AAU
AAC
AAA
AGU
AGC
AGA
Arg
Ser
Arg
Gly
ACGAUG AAG AGG
GUU
GUC
GUA
GUG
GCU
GCC
GCA
GCG
GAU
GAC
GAA
GAG
Val Ala
GGU
GGC
GGA
GGGGlu
Gly
G
U
C
A
Met orstart
UUG
G
The code is redundant!(>1 codon/aa)
Second mRNA base
Fir
st m
RN
A b
ase
(5 e
nd
of
cod
on
)
Th
ird
mR
NA
bas
e (3
en
d o
f co
do
n)
UUU
UUC
UUA
CUU
CUC
CUA
CUG
Phe
Leu
Leu
Ile
UCU
UCC
UCA
UCG
Ser
CCU
CCC
CCA
CCG
UAU
UACTyr
Pro
Thr
UAA Stop
UAG Stop
UGA Stop
UGU
UGCCys
UGG Trp
GC
U
U
C
A
U
U
C
C
CA
U
A
A
A
G
G
His
Gln
Asn
Lys
Asp
CAU CGU
CAC
CAA
CAG
CGC
CGA
CGG
G
AUU
AUC
AUA
ACU
ACC
ACA
AAU
AAC
AAA
AGU
AGC
AGA
Arg
Ser
Arg
Gly
ACGAUG AAG AGG
GUU
GUC
GUA
GUG
GCU
GCC
GCA
GCG
GAU
GAC
GAA
GAG
Val Ala
GGU
GGC
GGA
GGGGlu
Gly
G
U
C
A
Met orstart
UUG
G
The code is punctuated (start and stop)
4 Important Characteristics of the Genetic Code
• Triplet: 5’ to 3’ in mRNA• Universal • Punctuated• Redundant
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
Nontemplatestrand of DNA
RNA nucleotides
RNApolymerase
Templatestrand of DNA
3
35
5
5
3
Newly madeRNA
Direction of transcription
A
A A A
AA
A
T
TT
T
TTT G
GG
C
C C
CC
G
C CC A AA
U
U
U
end
Figure 17.7-4 Promoter
RNA polymeraseStart point
DNA
53
Transcription unit
35
Elongation
53
35
Nontemplate strand of DNA
Template strand of DNARNAtranscriptUnwound
DNA2
3535
3
RewoundDNA
RNAtranscript
5
Termination3
35
5Completed RNA transcript
Direction of transcription (“downstream”)
53
3
Initiation1
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
Promoter Nontemplate strand
15′3′
5′3′
Start point
RNA polymerase II
Templatestrand
TATA box
Transcriptionfactors
DNA3′5′
3′5′
3′5′
2
3
Transcription factors
RNA transcript
Transcription initiation complex
3′5′5′3′
A eukaryoticpromoter
Severaltranscriptionfactors bindto DNA.
Transcriptioninitiationcomplexforms.
T A T AAAA
TA A T T T T
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
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
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
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
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
5CapPre-mRNACodonnumbers
130 31104
mRNA 5Cap
5
Intron Exon
3 UTR
Introns cut out andexons spliced together
3
105 146
Poly-A tail
Codingsegment
Poly-A tail
UTR1146
The exons and introns are transcribed into RNA and then the exons are joined together at the RNA level:
Splicing
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
Spliceosome Small RNAs
Exon 2
Cut-outintron
Spliceosomecomponents
mRNA
Exon 1 Exon 2
Pre-mRNA
Exon 1
Intron
5′
5′
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
• 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 nucleicacid molecules
RNA secondary structure-illustrations
tRNA
U1 snRNA and snRNP
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 thanits number of genes
• More then one product from each gene• Adds flexibility
GeneDNA
Exon 1 Exon 2 Exon 3Intron Intron
Transcription
RNA processing
Translation
Domain 3
Domain 2
Domain 1
Polypeptide
Alternate splicing worksBecause genes and proteinsare made of modules
Exons = gene modulesDomains = protein modules
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?
Note Card Question (Review)
Promoter
RNA splicing/alternative splicing
Intron/exon
RNA secondary structure
Ribozyme
Protein domain
RNA World Hypothesis