Download The Genetic Code

Chapter
13
The Genetic Code
and Transcription
Lecture Presentation by
Dr. Cindy Malone,
California State University Northridge
© 2015 Pearson Education, Inc.
Section 13.1: The Genetic Code
 The genetic code: General features
– Written in linear form using ribonucleotide bases
that compose mRNA
– Each “word” consists of three ribonucleotide
letters, or a triplet code
 Codon: Every three ribonucleotides
– Unambiguous – each triplet specifies only one
amino acid
continued
© 2015 Pearson Education, Inc.
Section 13.1: The Genetic Code
continued
 The genetic code
– Degenerate: A given amino acid can be specified
by more than one triplet codon
– Contains “start” and “stop” signals: triplets that
initiate and terminate translation
© 2015 Pearson Education, Inc.
Section 13.1: The Genetic Code
continued
– Nonoverlapping: Any single ribonucleotide within
mRNA is part of one triplet
– Nearly universal: A single coding dictionary is
used by viruses, prokaryotes, archaea, and
eukaryotes
© 2015 Pearson Education, Inc.
Section 13.2: Operational Patterns
 mRNA – messenger RNA
– Serves as intermediate in transferring genetic
information from DNA to proteins
– Genetic information is stored in DNA
– Code that translates it to protein is in RNA
© 2015 Pearson Education, Inc.
Section 13.2: The Triplet Code
 Triplet code
– Provides 64 codons to specify 20 amino acids
© 2015 Pearson Education, Inc.
Section 13.2: Frameshift Mutations
 Reading frame
– Contiguous sequence of nucleotides
– Insertions or deletions shift reading frame and
change codons downstream  frameshift
mutation
 Triplet nature code was revealed by frameshift
mutations
(Figure 13-2)
© 2015 Pearson Education, Inc.
© 2015 Pearson Education, Inc.
Figure 13-2
© 2015 Pearson Education, Inc.
Figure 13-2a
© 2015 Pearson Education, Inc.
Figure 13-2b
Section 13.3: Triplet Binding Assay
 Triplet binding assay
– Developed by Nirenberg and Leder to determine
other specific codon assignments
– Ribosomes bind to single codon of three
nucleotides
– Complementary amino acid-charged tRNA can
bind (Figure 13-5 and Table 13.2)
© 2015 Pearson Education, Inc.
© 2015 Pearson Education, Inc.
Table 13.2
Section 13.3: Repeating Copolymers
 Chemically synthesized long RNAs
– Short repeating sequences enzymatically joined
short sequences together, which made long
RNAs
– Used for in vitro translation to determine more
codon assignments
– Figure 13-6 and Table 13.3
© 2015 Pearson Education, Inc.
Section 13.4: Degeneracy of the Genetic Code
 The genetic code is degenerate
– Many amino acids specified by more than one
codon
– Only tryptophan and methionine are encoded
by single codon (Figure 13-7)
– Genetic code shows order: chemically similar
amino acids share one or two middle bases in
triplets encoding them
© 2015 Pearson Education, Inc.
© 2015 Pearson Education, Inc.
Figure 13-7
Section 13.4: The Wobble Hypothesis
 The wobble hypothesis
– The initial two ribonucleotides of triplet codes are
often more critical than the third
– Third position
 Less spatially constrained
 Need not adhere as strictly to established base-pairing
rules
(Table 13.4)
© 2015 Pearson Education, Inc.
© 2015 Pearson Education, Inc.
Table 13.4
Section 13.4: Initiation
 Methionine (AUG) – initiator codon
– Initial amino acid incorporated into all proteins
– In bacteria: modified form of methionine
 N-formylmethionine (fmet)
 AUG: Only codon to encode methionine
– Appears internally in mRNA unformylated
© 2015 Pearson Education, Inc.
Section 13.4: Termination
 Termination codons: UAG, UAA, UGA
– Do not code for any amino acid
– Are not recognized by tRNA
– Translation terminates when these codons are
encountered
© 2015 Pearson Education, Inc.
Section 13.4: Nonsense Mutations
 Nonsense mutations
– Mutations that produce a stop codon internally in
gene
– Translation is terminated
– Partial polypeptide is produced
© 2015 Pearson Education, Inc.
Section 13.7: Overlapping Genes
 Overlapping genes
– Single mRNA has multiple initiation points
– Creates different reading frames
– Specifies more than one polypeptide
© 2015 Pearson Education, Inc.
Section 13.7: Open Reading Frames
 ORF: Open reading frame (overlapping
genes)
– DNA sequence produces RNA with start and stop
– Series of triplet codons specify amino acids to
make polypeptide
 In some viruses, initiation at different AUG
positions out of frame with another leads to
distinct polypeptides (Figure 13-8)
© 2015 Pearson Education, Inc.
© 2015 Pearson Education, Inc.
Figure 13-8
© 2015 Pearson Education, Inc.
Figure 13-8a
Section 13.8: Transcription
 Transcription
– RNA synthesized on DNA template
– Genetic information stored in DNA is transferred
to RNA
– Serves as intermediate molecule between DNA
and proteins
– Each triplet codon is complementary to anticodon
of tRNA
© 2015 Pearson Education, Inc.
VIDEO - TRANSCRIPCION
© 2015 Pearson Education, Inc.
Section 13.10: RNA Polymerase
 RNA polymerase
– Enzyme directs synthesis of RNA using DNA
template
– Nucleotides contain ribose, not deoxyribose
– No primer required for initiation
n(NTP)
DNA
RNA polymerase
© 2015 Pearson Education, Inc.
(NMP)n + n(PPi)
Section 13.10: Promoters
 Transcription results in ssRNA
– Template strand is transcribed
– Transcription begins with template binding by
RNA polymerase at promoter (Figure 13-9)
– Promoters: Specific DNA sequences in 5 region
upstream of initial transcription point
–  subunit responsible for promoter recognition
(initiation of transcription)
© 2015 Pearson Education, Inc.
VIDEO
 https://www.youtube.com/watch?v=SMtWvDbfHL
o&nohtml5=False
© 2015 Pearson Education, Inc.
© 2015 Pearson Education, Inc.
Figure 13-9
© 2015 Pearson Education, Inc.
Figure 13-9a
© 2015 Pearson Education, Inc.
Figure 13-9b
© 2015 Pearson Education, Inc.
Figure 13-9c
Section 13.10: Transcription Start Site
 Transcription start site
– DNA double helix is denatured: unwound to make
template strand accessible for RNA polymerase
– Interaction of promoters and RNA polymerase
regulates efficiency of transcription
© 2015 Pearson Education, Inc.
Section 13.10: Consensus Sequences
 Consensus sequences
– DNA sequences homologous in different genes of
same organism
 E. coli promoters have two consensus
sequences
– TTGACA and TATAAT (Pribnow box)
– Positioned at 35 and 10 with respect to the
transcription initiation site
© 2015 Pearson Education, Inc.
Section 13.10: Chain Elongation
 Chain elongation
– Ribosomes are added to RNA chain
–  subunit dissociates from holoenzyme
– Elongation proceeds under direction of core
enzyme
(Figure 13-9c)
© 2015 Pearson Education, Inc.
© 2015 Pearson Education, Inc.
Figure 13-9
Section 13.10: Termination
 Termination
– Enzyme traverses entire gene until a termination
nucleotide sequence is encountered
– In bacteria: Termination transcribed into RNA
causes newly formed transcript to fold back on
itself (hairpin)
– At times, termination depends on the rho ()
termination factor
© 2015 Pearson Education, Inc.
13.11 Transcription in Eukaryotes Differs
from Prokaryotic Transcription in Several
Ways
© 2015 Pearson Education, Inc.
Section 13.11: Eukaryotic Transcription
 Transcription in eukaryotes
– Occurs within nucleus (unlike prokaryotes)
– mRNA must leave nucleus for translation
– Chromatin remodeling: Chromatin must uncoil to
make DNA accessible to RNA Pol
– RNA polymerases rely on transcription factors
(TFs) to scan/bind DNA
– Enhancers and silencers control transcription
regulation
© 2015 Pearson Education, Inc.
Section 13.11: RNA Polymerases
 Eukaryotes possess three forms of RNA
polymerase
– Each transcribes different types of genes
(Table 13.7)
– RNA Pol I
– RNA Pol II
– RNA Pol III
© 2015 Pearson Education, Inc.
© 2015 Pearson Education, Inc.
Table 13.7
Section 13.11: RNA Pol II
 RNA polymerase II (RNAP II)
– Responsible for transcription of wide range of
genes in eukaryotes
– Activity of RNAP II is dependent on cis-acting
elements and trans-acting transcription factors
– RNAP II core-promoter determines where RNAP
II binds to DNA
© 2015 Pearson Education, Inc.
Section 13.11: TATA Box
 Regulatory sequences influence efficiency of
transcription initiation by RNAP II
– Proximal-promoter elements
– Enhancers
– Silencers
 TATA box
– Core-promoter element
– Binds TATA-binding protein (TBP) of
transcription factor TFIID: determines start
transcription start site
© 2015 Pearson Education, Inc.
Section 13.11: Enhancers and Silencers
 Enhancers and silencers
– Found upstream, within, or downstream of gene
– Enhancers increase transcription levels; silencers
decrease them
– Modulate transcription from a distance
– Act to increase or decrease transcription in
response to cell’s requirement for gene product
© 2015 Pearson Education, Inc.
Section 13.11: Transcription Factors
 Transcription factors facilitate RNAP II binding
and initiation of transcription
– General transcription factors: Required for all
RNAP II-mediated transcription
– Transcription activators and repressors:
Influence efficiency or rate of RNAP II
transcription initiation
© 2015 Pearson Education, Inc.
Section 13.11: Cap and Tail
 Eukaryotic mRNAs require processing to
produce mature mRNAs
 Posttranscriptional modifications
– Addition of 5 cap (7-mG cap)
– Addition of 3 tail (poly-A tail)
– Excision of introns
(Figure 13-10)
© 2015 Pearson Education, Inc.
© 2015 Pearson Education, Inc.
Figure 13-10
13.12 The Coding Regions of Eukaryotic
Genes Are Interrupted by Intervening
Sequences
© 2015 Pearson Education, Inc.
Section 13.12: Introns and Exons
 Introns (intervening sequences)
– Regions of initial RNA transcript not expressed in
amino acid sequence of protein
– DNA sequences not represented in final mRNA
product
– Exons are sequence retained and expressed
– Prokaryotes do not have introns
– Heteroduplexes: Introns present in DNA but not
mRNA loop out (Figure 13-11)
© 2015 Pearson Education, Inc.
© 2015 Pearson Education, Inc.
Figure 13-11
Section 13.12: Splicing
 Posttranscriptional modification: Splicing
– Introns are removed by splicing
– Exons are then joined together in mature mRNA
– Mature mRNA is smaller than initial RNA
(Figure 13-12 and Table 13.8)
© 2015 Pearson Education, Inc.
© 2015 Pearson Education, Inc.
Figure 13-12
Section 13.12: Self-Splicing RNAs and
Spliceosome
 Self-Splicing RNAs
– Self-excision group I introns occurs in bacteria,
lower eukaryotes, and higher plants
(Figure 13-13d)
 Spliceosome
– Pre-mRNA introns spliced out by spliceosome
– Reaction involves formation of lariat structure
(Figure 13-14)
© 2015 Pearson Education, Inc.
© 2015 Pearson Education, Inc.
Figure 13-13
© 2015 Pearson Education, Inc.
Figure 13-14
© 2015 Pearson Education, Inc.
Figure 13-15