Insert Fig CO 8.

Insert Fig CO 8

Terminology Genetics: the study of what genes are, how they carry information, how information is expressed, and how genes are replicated Gene: a segment of DNA that encodes a functional product, usually a protein Chromosome: structure containing DNA that physically carries hereditary information; the chromosomes contain the genes Genome: all the genetic information in a cell

Terminology Genomics: the molecular study of genomes
Genotype: the genes of an organism Phenotype: expression of the genes

Chromosome Insert Fig 8.1a Disrupted E. coli cell
Figure 8.1a A prokaryotic chromosome. Chromosome Insert Fig 8.1a Disrupted E. coli cell

Genetic map of the chromosome of E. coli
Figure 8.1b A prokaryotic chromosome. Insert Fig 8.1b Amino acid metabolism DNA replication and repair Lipid metabolism Carbohydrate metabolism Membrane synthesis KEY Genetic map of the chromosome of E. coli

expression replication recombination Insert Fig 8.2
Figure 8.2 The Flow of Genetic Information. Parent cell DNA expression recombination replication Genetic information is used within a cell to produce the proteins needed for the cell to function. Insert Fig 8.2 Genetic information can be transferred between cells of the same generation. Genetic information can be transferred between generations of cells. New combinations of genes Transcription Translation Cell metabolizes and grows Recombinant cell Daughter cells

DNA Polymer of nucleotides: adenine, thymine, cytosine, and guanine
Double helix associated with proteins “Backbone” is deoxyribose-phosphate Strands are held together by hydrogen bonds between AT and CG Strands are antiparallel

Insert Fig 8.3b Figure 8.3b DNA replication.
5′ end 3′ end Insert Fig 8.3b 3′ end 5′ end The two strands of DNA are antiparallel. The sugar-phosphate backbone of one strand is upside down relative to the backbone of the other strand. Turn the book upside down to demonstrate this.

Insert Fig 8.3a Figure 8.3a DNA replication. The replication fork
5′ end 3′ end Parental strand Parental strand 1 1 1 The double helix of the parental DNA separates as weak hydrogen bonds between the nucleotides on opposite strands break in response to the action of replication enzymes. Replication fork Insert Fig 8.3a 2 2 Hydrogen bonds form between new complementary nucleotides and each strand of the parental template to form new base pairs. 2 3 3 Enzymes catalyze the formation of sugar-phosphate bonds between sequential nucleotides on each resulting daughter strand. Daughter strand 5′ end Parental strand 3′ end Parental strand Daughter strand forming The replication fork

Insert Fig 8.4 New Template Strand Strand Sugar Phosphate
1 Insert Fig 8.4 2 Hydrolysis of the phosphate bonds provides the energy for the reaction. When a nucleoside triphosphate bonds to the sugar, it loses two phosphates.

DNA Synthesis DNA is copied by DNA polymerase In the 5'  3' direction
Initiated by an RNA primer Leading strand is synthesized continuously Lagging strand is synthesized discontinuously Okazaki fragments RNA primers are removed and Okazaki fragments joined by a DNA polymerase and DNA ligase

Table 8.1 Important Enzymes in DNA Replication, Expression, and Repair
Insert Table 8.1

Figure 8.5 A summary of events at the DNA replication fork.
Proteins stabilize the unwound parental DNA. The leading strand is synthesized continuously by DNA polymerase. 3' DNA polymerase 5' Enzymes unwind the parental double helix. 1 Replication fork Insert Fig 8.5 RNA primer Primase 5' DNA polymerase 3' Okazaki fragment DNA ligase Parental strand 3' DNA polymerase 5' The lagging strand is synthesized discontinuously. Primase, an RNA polymerase, synthesizes a short RNA primer, which is then extended by DNA polymerase. DNA polymerase digests RNA primer and replaces it with DNA. DNA ligase joins the discontinuous fragments of the lagging strand.

Figure 8.6 Replication of bacterial DNA.
Replication forks REPLICATION An E. coli chromosome in the process of replicating 1 Origin of replication Parental strand Daughter strand Replication fork Replication fork Termination of replication Bidirectional replication of a circular bacterial DNA molecule

Transcription DNA is transcribed to make RNA (mRNA, tRNA, and rRNA)
Transcription begins when RNA polymerase binds to the promoter sequence Transcription proceeds in the 5'  3' direction Transcription stops when it reaches the terminator sequence

Insert Fig 8.7 Figure 8.7 The process of transcription. RNA polymerase
DNA TRANSCRIPTION DNA mRNA 1 RNA polymerase bound to DNA Protein Promoter (gene begins) Template strand of DNA RNA polymerase 1 RNA polymerase binds to the promoter, and DNA unwinds at the beginning of a gene. Insert Fig 8.7 2 RNA is synthesized by complementary base pairing of free nucleotides with the nucleotide bases on the template strand of DNA. RNA RNA nucleotides 3 The site of synthesis moves along DNA; DNA that has been transcribed rewinds. RNA synthesis 4 Transcription reaches the terminator. Terminator (gene ends) 5 RNA and RNA polymerase are released, and the DNA helix re-forms.

Insert Fig 8.11 Figure 8.11 RNA processing in eukaryotic cells. Exon
Intron Exon RNA polymerase Intron Exon DNA Met Met In the nucleus, a gene composed of exons and introns is transcribed to RNA by RNA polymerase. 1 DNA Met RNA transcript 2 Processing involves snRNPs in the nucleus to remove the intron-derived RNA and splice together the exon- derived RNA into mRNA. 1 Insert Fig 8.11 mRNA Met After further modification, the mature mRNA travels to the cytoplasm, where it directs protein synthesis. 3 Met Nucleus Cytoplasm

Translation mRNA is translated in codons (three nucleotides)
Translation of mRNA begins at the start codon: AUG Translation ends at nonsense codons: UAA, UAG, UGA

The Genetic Code 64 sense codons on mRNA encode the 20 amino acids
The genetic code is degenerate tRNA carries the complementary anticodon

Figure 8.8 The genetic code.
Insert Fig 8.8

Figure 8.10 Simultaneous transcription and translation in bacteria.
RNA polymerase DNA Met Met Met mRNA DNA Met Protein RNA Ribosome Peptide 1 Insert Fig 8.10 Met Met Met Met Direction of transcription RNA polymerase DNA 5′ Peptide Polyribosome Ribosome mRNA Direction of translation

Insert Fig 8.9 (1) and (2) Figure 8.9.1-2 The process of translation.
RNA polymerase TRANSLATION Ribosome DNA Met DNA Leu mRNA Met Ribosomal subunit P Site tRNA Protein Anticodon 1 Ribosomal subunit Start codon Second codon mRNA mRNA 1 Components needed to begin translation come together. Insert Fig 8.9 (1) and (2) 2 On the assembled ribosome, a tRNA carrying the first amino acid is paired with the start codon on the mRNA. The place where this first tRNA sits is called the P site. A tRNA carrying the second amino acid approaches.

Peptide bond forms Met Met Phe Met Leu DNA A site Met Leu Gly E site 1 mRNA mRNA Ribosome moves along mRNA 3 The second codon of the mRNA pairs with a tRNA carrying the second amino acid at the A site. The first amino acid joins to the second by a peptide bond. This attaches the polypeptide to the tRNA in the P site. 4 The ribosome moves along the mRNA until the second tRNA is in the P site. The next codon to be translated is brought into the A site. The first tRNA now occupies the E site. Insert Fig 8.9 (3) and (4)

tRNA released Met Growing polypeptide chain Met Leu Gly Leu Phe Gly Met Phe mRNA Insert Fig 8.9 (5) and (6) mRNA 5 The second amino acid joins to the third by another peptide bond, and the first tRNA is released from the E site. 6 The ribosome continues to move along the mRNA, and new amino acids are added to the polypeptide.

Polypeptide released Met Phe Gly Met Arg Met Leu Leu Gly Gly Met Met Leu Met Phe Phe Gly Gly Leu Leu Leu Met Phe Gly Met mRNA Arg New protein Insert Fig 8.9 (7) and (8) mRNA Stop codon 7 When the ribosome reaches a stop codon, the polypeptide is released. 8 Finally, the last tRNA is released, and the ribosome comes apart. The released polypeptide forms a new protein.

Regulation Constitutive genes are expressed at a fixed rate
Other genes are expressed only as needed Inducible genes Repressible genes Catabolite repression

I P O Z Y A 1 Figure 8.12.1 An inducible operon. Operon Control region
Structural genes I P O Z Y A DNA Regulatory gene Promoter Operator 1 Structure of the operon. The operon consists of the promoter (P) and operator (O) sites and structural genes that code for the protein. The operon is regulated by the product of the regulatory gene (I ).

Transcription Translation RNA polymerase Repressor Active mRNA
Figure An inducible operon. RNA polymerase Transcription Repressor mRNA Active repressor protein Translation Repressor active, operon off. The repressor protein binds with the operator, preventing transcription from the operon.

Transcription Translation Operon mRNA
Figure An inducible operon. Transcription Operon mRNA Translation Allolactose (inducer) Inactive repressor protein Transacetylase Permease β-Galactosidase Repressor inactive, operon on. When the inducer allolactose binds to the repressor protein, the inactivated repressor can no longer block transcription. The structural genes are transcribed, ultimately resulting in the production of the enzymes needed for lactose catabolism.

Figure 8.13.1 A repressible operon.
Control region Structural genes DNA Regulatory gene Promoter Operator Structure of the operon. The operon consists of the promoter (P) and operator (O) sites and structural genes that code for the protein. The operon is regulated by the product of the regulatory gene (I ).

Transcription Translation
Figure A repressible operon. RNA polymerase Transcription Repressor mRNA Operon mRNA Translation Polypeptides comprising the enzymes for tryptophan synthesis Inactive repressor protein Repressor inactive, operon on. The repressor is inactive, and transcription and translation proceed, leading to the synthesis of tryptophan.

Repressor active, operon off. When the corepressor
Figure A repressible operon. Active repressor protein Tryptophan (corepressor) Repressor active, operon off. When the corepressor tryptophan binds to the repressor protein, the activated repressor binds with the operator, preventing transcription from the operon.

Mutation A change in the genetic material
Mutations may be neutral, beneficial, or harmful Mutagen: agent that causes mutations Spontaneous mutations: occur in the absence of a mutagen

Mutation Base substitution (point mutation) Change in one base

Insert Fig 8.17 Figure 8.17 Base substitutions. Parental DNA
Replication During DNA replication, a thymine is incorporated opposite guanine by mistake. Daughter DNA Daughter DNA Daughter DNA In the next round of replication, adenine pairs with the new thymine, yielding an AT pair in place of the original GC pair. Replication Insert Fig 8.17 Granddaughter DNA When mRNA is transcribed from the DNA containing this substitution, a codon is produced that, during translation, encodes a different amino acid: tyrosine instead of cysteine. Transcription mRNA Translation Amino acids Cysteine Tyrosine Cysteine Cysteine

Mutation Missense mutation
Base substitution results in change in amino acid 37

Normal DNA molecule Missense mutation
Figure 8.18a-b Types of mutations and their effects on the amino acid sequences of proteins. DNA (template strand) Transcription mRNA Translation Amino acid sequence Met Lys Phe Gly Stop Normal DNA molecule DNA (template strand) mRNA Amino acid sequence Met Lys Phe Ser Stop Missense mutation

Mutation Nonsense mutation
Base substitution results in a nonsense codon

Normal DNA molecule Nonsense mutation
Figure 8.18ac Types of mutations and their effects on the amino acid sequences of proteins. DNA (template strand) Transcription mRNA Translation Amino acid sequence Met Lys Phe Gly Stop Normal DNA molecule Met Stop Nonsense mutation

Mutation Frameshift mutation
Insertion or deletion of one or more nucleotide pairs

Normal DNA molecule Frameshift mutation
Figure 8.18ad Types of mutations and their effects on the amino acid sequences of proteins. DNA (template strand) Transcription mRNA Translation Amino acid sequence Met Lys Phe Gly Stop Normal DNA molecule Met Lys Leu Ala Frameshift mutation

Genetic Recombination
Vertical gene transfer: occurs during reproduction between generations of cells

Horizontal gene transfer: the transfer of genes between cells of the same generation 45

Exchange of genes between two DNA molecules Crossing over occurs when two chromosomes break and rejoin

Donor DNA Recipient chromosome Insert Fig 8.24 RecA protein
Figure 8.24 Genetic recombination by crossing over. DNA from one cell aligns with DNA in the recipient cell. Notice that there is a nick in the donor DNA. Donor DNA Recipient chromosome DNA from the donor aligns with complementary base pairs in the recipient’s chromosome. This can involve thousands of base pairs. Insert Fig 8.24 RecA protein catalyzes the joining of the two strands. RecA protein The result is that the recipient’s chromosome contains new DNA. Complementary base pairs between the two strands will be resolved by DNA polymerase and ligase. The donor DNA will be destroyed. The recipient may now have one or more new genes.

Mating bridge Sex pilus F– cell Insert Fig 8.27 F+ cell Sex pilus
Figure 8.27 Bacterial conjugation. Mating bridge Sex pilus F– cell Insert Fig 8.27 F+ cell Sex pilus Mating bridge

Figure 8.28a Conjugation in E. coli.
RECOMBINATION Bacterial chromosome Mating bridge Replication and transfer of F factor Insert Fig 8.28a F factor F+ cell F– cell F+ cell F+ cell When an F factor (a plasmid) is transferred from a donor (F+) to a recipient (F–), the F– cell is converted to an F+ cell.

Figure 8.28b Conjugation in E. coli.
Recombination between F factor and chromosome, occurring at a specific site on each Insertion of F factor into chromosome Integrated F factor Insert Fig 8.28b F+ cell Hfr cell When an F factor becomes integrated into the chromosome of an F+ cell, it makes the cell a high frequency of recombination (Hfr) cell.

Insert Fig 8.1b Figure 8.1b A prokaryotic chromosome.
Amino acid metabolism DNA replication and repair Lipid metabolism Carbohydrate metabolism Membrane synthesis KEY

Insert Fig 8.29 Figure 8.29 Transduction by a bacteriophage.
RECOMBINATION Phage protein coat Phage DNA Bacterial chromosome A phage infects the donor bacterial cell. Donor cell Phage DNA and proteins are made, and the bacterial chromosome is broken into pieces. Occasionally during phage assembly, pieces of bacterial DNA are packaged in a phage capsid. Then the donor cell lyses and releases phage particles containing bacterial DNA. Insert Fig 8.29 Phage DNA A phage carrying bacterial DNA infects a new host cell, the recipient cell. Bacterial DNA Recipient cell Donor bacterial DNA Recipient bacterial DNA 5 Recombination can occur, producing a recombinant cell with a genotype different from both the donor and recipient cells. Recombinant cell reproduces normally Many cell divisions © 2013 Pearson Education, Inc.

Plasmids Conjugative plasmid: carries genes for sex pili and transfer of the plasmid Dissimilation plasmids: encode enzymes for catabolism of unusual compounds R factors: encode antibiotic resistance

Insert Fig 8.30 Figure 8.30 R factor, a type of plasmid.
Origin of replication mer sul str Pilus and conjugation proteins cml Insert Fig 8.30 Origin of transfer tet

Genes and Evolution Mutations and recombination provide diversity
Fittest organisms for an environment are selected by natural selection

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