The structure of DNA The structure of DNA Deoxyribonucleic acid Deoxyribonucleic acid DNA is made of nucleotides DNA is made of nucleotides Each nucleotide is composed of Each nucleotide is composed of phosphate, sugar (deoxyribose) and a phosphate, sugar (deoxyribose) and a nitrogen base nitrogen base 4 nitrogen bases – Adenine, Thymine, 4 nitrogen bases – Adenine, Thymine, Guanine, Cytosine (A,T,G,C) Guanine, Cytosine (A,T,G,C) A-T, C-G A-T, C-G Bases are linked by hydrogen bonds Bases are linked by hydrogen bonds
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The structure of DNA Deoxyribonucleic acid DNA is made of nucleotides Each nucleotide is composed of phosphate, sugar (deoxyribose) and a nitrogen.
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The structure of DNAThe structure of DNA
Deoxyribonucleic acidDeoxyribonucleic acid DNA is made of nucleotidesDNA is made of nucleotides Each nucleotide is composed of phosphate, Each nucleotide is composed of phosphate,
sugar (deoxyribose) and a nitrogen basesugar (deoxyribose) and a nitrogen base 4 nitrogen bases – Adenine, Thymine, Guanine, 4 nitrogen bases – Adenine, Thymine, Guanine,
Cytosine (A,T,G,C)Cytosine (A,T,G,C) A-T, C-GA-T, C-G Bases are linked by hydrogen bondsBases are linked by hydrogen bonds
Figure 16.5 Sugar–phosphatebackbone
Nitrogenous bases
Thymine (T)
Adenine (A)
Cytosine (C)
Guanine (G)
Nitrogenous base
Phosphate
DNA nucleotide
Sugar(deoxyribose)
3 end
5 end
Figure 16.7
3.4 nm
1 nm
0.34 nm
Hydrogen bond
(a) Key features ofDNA structure
Space-fillingmodel
(c)(b) Partial chemical structure
3 end
5 end
3 end
5 end
T
T
A
A
G
G
C
C
C
C
C
C
C
C
C
C
C
G
G
G
G
G
G
G
G
G
T
T
T
T
T
T
A
A
A
A
A
A
Base PairingBase Pairing
DNA strandsDNA strands
Run in opposite directionsRun in opposite directions Helicase – unwinds helixHelicase – unwinds helix Topoisomerase – cuts and rejoins the helixTopoisomerase – cuts and rejoins the helix Ligase – brings together Okazaki fragmentsLigase – brings together Okazaki fragments DNA polymerases add nucleotides only to the DNA polymerases add nucleotides only to the
free 3free 3end of a growing strand; therefore, a end of a growing strand; therefore, a new DNA strand can elongate only in the new DNA strand can elongate only in the 55toto33directiondirection
Along one template strand of DNA, the DNA Along one template strand of DNA, the DNA polymerase synthesizes a polymerase synthesizes a leading strand leading strand continuously, moving toward the replication forkcontinuously, moving toward the replication fork
To elongate the other new strand, called the To elongate the other new strand, called the lagging strandlagging strand, DNA polymerase must work in , DNA polymerase must work in the direction away from the replication forkthe direction away from the replication fork
The lagging strand is synthesized as a series of The lagging strand is synthesized as a series of segments called segments called Okazaki fragmentsOkazaki fragments, which are , which are joined together by joined together by DNA ligaseDNA ligase
The transfer of genetic info. From DNA to The transfer of genetic info. From DNA to messenger RNA (mRNA)messenger RNA (mRNA)
2.2. TranslationTranslation
The transfer of mRNA to proteinThe transfer of mRNA to protein
GenesGenes are pieces of DNA that code for proteins are pieces of DNA that code for proteins
mRNA – Uracil instead of ThyminemRNA – Uracil instead of Thymine
TranscriptionTranscription
DNA codes for single strand of mRNADNA codes for single strand of mRNA This happens in the nucleusThis happens in the nucleus RNA polymerase binds to the promoter RNA polymerase binds to the promoter
region on DNA templateregion on DNA template Sigma factor recognizes binding site on Sigma factor recognizes binding site on
DNADNA mRNA detatches at the terminator region mRNA detatches at the terminator region
of the DNA templateof the DNA template
TranscriptionTranscription
TranslationTranslation
The transfer of mRNA into a proteinThe transfer of mRNA into a protein This happens at the ribosomeThis happens at the ribosome Every 3 base pairs of mRNA is called a Every 3 base pairs of mRNA is called a
codoncodon tRNA hold anti-codons and amino acidstRNA hold anti-codons and amino acids tRNA bring amino acids down to the tRNA bring amino acids down to the
ribosomes using the corresponding anti-ribosomes using the corresponding anti-codon.codon.
TranslationTranslation
TranslationTranslation
The Genetic CodeThe Genetic Code
Discovery of DNA – Rosalind Discovery of DNA – Rosalind FranklinFranklin
Watson and CrickWatson and Crick
MutationsMutations
Sickle cell mutationSickle cell mutation
Prokaryotes vs. EukaryotesProkaryotes vs. Eukaryotes
In prokaryotes, translation of mRNA can In prokaryotes, translation of mRNA can begin before transcription has finishedbegin before transcription has finished
In a eukaryotic cell, the nuclear envelope In a eukaryotic cell, the nuclear envelope separates transcription from translation separates transcription from translation
Eukaryotic RNA transcripts are modified Eukaryotic RNA transcripts are modified through RNA processing to yield the finished through RNA processing to yield the finished mRNAmRNA
A A primary transcript primary transcript is the initial RNA is the initial RNA transcript from any gene prior to processingtranscript from any gene prior to processing
Comparing Gene Expression in Bacteria, Archaea, and Eukarya
• Bacteria and eukarya differ in their RNA polymerases, termination of transcription, and ribosomes; archaea tend to resemble eukarya in these respects
• Bacteria can simultaneously transcribe and translate the same gene
• In eukarya, transcription and translation are separated by the nuclear envelope
• In archaea, transcription and translation are likely coupled
Important vocabulary in Important vocabulary in transcriptiontranscription
The stretch of DNA that is transcribed is called a The stretch of DNA that is transcribed is called a transcription unittranscription unit
Transcription factors (sigma) – initiate the Transcription factors (sigma) – initiate the binding of the RNA polymerasebinding of the RNA polymerase
The completed assembly of transcription factors The completed assembly of transcription factors and RNA polymerase II bound to a promoter is and RNA polymerase II bound to a promoter is called a called a transcription initiation complextranscription initiation complex
A promoter called a A promoter called a TATA box TATA box is crucial in is crucial in forming the initiation complex in eukaryotesforming the initiation complex in eukaryotes
Figure 17.8
Transcription initiationcomplex forms
3
DNAPromoter
Nontemplate strand
53
53
53
Transcriptionfactors
RNA polymerase II
Transcription factors
53
53
53
RNA transcript
Transcription initiation complex
5 3
TATA box
T
T T T T T
A A A AA
A A
T
Several transcriptionfactors bind to DNA
2
A eukaryotic promoter1
Start point Template strand
RNA processing
• Enzymes in the eukaryotic nucleus modify pre-mRNA (RNA processing) before the genetic messages are dispatched to the cytoplasm
• During RNA processing, both ends of the primary transcript are usually altered
• Also, usually some interior parts of the molecule are cut out, and the other parts spliced together
• Each end of a pre-mRNA molecule is modified in a particular way
– The 5 end receives a modified nucleotide 5 cap
– The 3 end gets a poly-A tail• These modifications share several functions
– They seem to facilitate the export of mRNA to the cytoplasm
– They protect mRNA from hydrolytic enzymes– They help ribosomes attach to the 5 end
Figure 17.10
Protein-codingsegment
Polyadenylationsignal
5 3
35 5Cap UTRStartcodon
G P P P
Stopcodon
UTR
AAUAAA
Poly-A tail
AAA AAA…
RNA Splicing
• In some cases, RNA splicing is carried out by spliceosomes
• Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites
Figure 17.12-3RNA transcript (pre-mRNA)
5Exon 1
Protein
snRNA
snRNPs
Intron Exon 2
Other proteins
Spliceosome
5
Spliceosomecomponents
Cut-outintronmRNA
5Exon 1 Exon 2
GeneDNA
Exon 1 Exon 2 Exon 3Intron Intron
Transcription
RNA processing
Translation
Domain 3
Domain 2
Domain 1
Polypeptide
Figure 17.13
Figure 17.15
Amino acidattachmentsite
3
5
Hydrogenbonds
Anticodon
(a) Two-dimensional structure (b) Three-dimensional structure(c) Symbol used
in this book
Anticodon Anticodon3 5
Hydrogenbonds
Amino acidattachmentsite5
3
A A G
Figure 17.22
Ribosome
mRNA
Signalpeptide
SRP
1
SRPreceptorprotein
Translocationcomplex
ERLUMEN
2
3
45
6
Signalpeptideremoved
CYTOSOL
Protein
ERmembrane
What Is a Gene? Revisiting the Question
• The idea of the gene has evolved through the history of genetics
• We have considered a gene as– A discrete unit of inheritance
– A region of specific nucleotide sequence in a chromosome
– A DNA sequence that codes for a specific polypeptide chain