Download presentation
Presentation is loading. Please wait.
Published byMeredith Holmes Modified over 7 years ago
1
I. The Blueprint of Life: Structure of the Bacterial Genome
4.3 Genetic Elements: Chromosomes and Plasmids
2
4.3 Genetic Elements: Chromosomes and Plasmids
Genome: entire complement of genes in cell or virus Chromosome: main genetic element in prokaryotes, usually a single piece of DNA Other genetic elements include virus genomes, plasmids, transposable elements (jumping genes) and in eukaryotes-genomes of organelles
3
4.3 Genetic Elements: Chromosomes and Plasmids
Viruses may be either RNA or DNA Plasmids: replicate separately from chromosome Great majority are double-stranded Most are circular Generally beneficial for the cell (e.g., antibiotic resistance) NOT extracellular, unlike viruses “autonomous” “episome”
4
4.3 Genetic Elements: Chromosomes and Plasmids
Chromosome is a genetic element with "housekeeping" genes Presence of essential genes is necessary for a genetic element to be called a chromosome Plasmid is a genetic element that is expendable and rarely contains genes for growth under all conditions-extra genes
5
4.3 Genetic Elements: Chromosomes and Plasmids
Transposable elements Segment of DNA that can move from one site to another site on the same or a different DNA molecule Inserted into other DNA molecules Three main types: Insertion sequences (IS) Transposons (Tn) Certain viruses
6
4.3 Genetic Elements: Chromosomes and Plasmids
The Escherichia coli chromosome Escherichia coli is a useful model organism for the study of biochemistry, genetics, and bacterial physiology The E. coli chromosome from strain MG1655 has been mapped using a combination of biological and biochemical methods (Figure 4.8)
7
Figure 4.8 The chromosome of Escherichia coli strain K-12.
8
4.3 Genetic Elements: Chromosomes and Plasmids
Some features of the E. coli chromosome Many genes encoding enzymes of a single biochemical pathway are clustered into groups called operons Operons are equally distributed on both strands ~5 Mbp in size (entire chromosome) ~40% of predicted proteins are of unknown function Average protein contains ~300 amino acids Genes are close together Few repeated genes Few intervening sequences or introns
9
4.3 Genetic Elements: Chromosomes and Plasmids
Plasmids: genetic elements that replicate independently of the host chromosome (Figure 4.9) Small circular or linear DNA molecules Range in size from 1 kbp to >1 Mbp; typically less than 5% of the size of the chromosome Carry a variety of nonessential, but often very helpful, genes Abundance (copy number) is variable: relaxed vs stringent
10
Figure 4.9 The bacterial chromosome and bacterial plasmids, as seen in the electron microscope.
11
4.3 Genetic Elements: Chromosomes and Plasmids
A cell can contain more than one plasmid Genetic information encoded on plasmids is not essential for cell function under all conditions BUT may confer a selective growth advantage under certain conditions
12
4.3 Genetic Elements: Chromosomes and Plasmids
R plasmids Resistance plasmids; confer resistance to antibiotics and other growth inhibitors (Figure 4.10) Widespread and well-studied group of plasmids Many code for conjugation functions: they can move into a new cell through conjugation
13
Figure 4.10 Genetic map of the resistance plasmid R100.
14
4.3 Genetic Elements: Chromosomes and Plasmids
In several pathogenic bacteria, virulence characteristics are encoded by plasmid genes Virulence factors Enable pathogen to colonize Enable pathogen to cause host damage Hemolysin Enterotoxin
15
4.3 Genetic Elements: Chromosomes and Plasmids
Bacteriocins Proteins produced by bacteria that inhibit or kill closely related species or even different strains of the same species Colicin, nisin Genes encoding bacteriocins are often carried on plasmids
16
4.7 Transcription Transcription (DNA to RNA) is carried out by RNA polymerase (Rpol) using DNA as template with RNA chain growth in 5’ to 3’ direction. Transciption begins at a DNA sequence called a promoter. Also requires sigma factor or start factor. Transcription stops at specific sites called transcription terminators
17
Gene(s) to be transcribed
RNA polymerase (core enzyme) Sigma factor Sigma recognizes promoter and initiation site. 5′ 3′ 3′ 5′ Promoter region Gene(s) to be transcribed (light green strand) Transcription begins; sigma released. RNA chain grows. Sigma 5′ 3′ 3′ 5′ 5′ RNA 5′ 3′ 3′ 5′ Termination site reached; chain growth stops. 5′ 5′ 3′ 3′ 5′ 5′ Figure 4.20 Transcription. Polymerase and RNA released. 5′ 3′ 3′ 5′ 3′ 5′ DNA Short transcripts Longer transcripts Figure 4.20
18
Figure 4.22 RNA polymerase (core enzyme) Transcription 5′ 3′ 3′ 5′
Sigma mRNA start 5′ 3′ 1. C T T G A G A T C T T G C A C G C T A G A G T A T G C T G A C T G A A C G T A T G T A C T A C G A C T G T C A G C A T C T G A A G C T A T C A G T T G C A T C G T A C T T A C A G T A G C G A T A T C G G A C T G C A C G G A C G A C G A T A C T A C G T 2. Figure 4.22 The interaction of RNA polymerase with a bacterial promoter. 3. 4. 5. 6. –35 region Pribnow box Consensus T T G A C A T A T A A T Promoter sequence Figure 4.22
19
4.7 Transcription Consensus promoter sequence
Pribnow Box and -35 region Core enzyme and holoenzyme Transcription start site Upstream and downstream
20
4.7 Transcription Termination of RNA synthesis is governed by a specific DNA sequence Intrinsic terminators: transcription is terminated without any additional factors Rho-dependent termination: Rho protein recognizes specific DNA sequences and causes a pause in the RNA polymerase
21
4.9 Transcription in Archaea and Eukarya
The Archaea contain only a single RNA polymerase Resembles eukaryotic polymerase II (Figure 4.21)
22
Figure 4.21 Bacteria Archaea Eukarya α β β' ω
Figure 4.21 RNA polymerase from the three domains. Figure 4.21
23
4.9 Transcription in Archaea and Eukarya
Archaea have a simplified version of eukaryotic transcription apparatus Promoters and RNA polymerase similar to eukaryotes (Figure 4.26) Regulation of transcription has major similarities with Bacteria
24
4.9 Transcription in Archaea and Eukarya
Eukaryotic genes have coding and noncoding regions Exons are the coding sequences Introns are the intervening sequences Are rare in Archaea Are found in tRNA and rRNA genes of Archaea Archaeal introns excised by special endonuclease (Figure 4.27)
25
4.9 Transcription in Archaea and Eukarya
Eukaryotic RNA processing: many RNA molecules are altered before they carry out their role in the cell RNA splicing Takes place in nucleus Removes introns from RNA transcripts Performed by the spliceosome (Figure 4.28)
26
4.9 Transcription in Archaea and Eukarya
Eukaryotic RNA processing (cont'd) RNA capping (Figure 4.29) Addition of methylated guanine to 5′ end of mRNA Poly(A) tail (Figure 4.29) Addition of 100–200 adenylate residues Stabilizes mRNA and is required for translation
27
4.11 Translation and the Genetic Code
Transfer RNA aka tRNA acts as the adaptor
28
4.11 Translation and the Genetic Code
Codon-anticodon interaction is base-pairing
29
4.11 Translation and the Genetic Code
3′ Wobble: irregular base pairing allowed at third position of tRNA (Figure 4.32) 5′ Alanine tRNA aka alanyl-tRNA Anticodon C G G Wobble position; base pairing more flexible here Key bases in codon: anticodon pairing Figure 4.32 The wobble concept. 5′ G C U 3′ mRNA Codon Figure 4.32
31
4.11 Translation and the Genetic Code
Codon bias: multiple codons for the same amino acid are not used equally Varies with organism Correlated with tRNA availability Cloned genes from one organism may not be translated by recipient organism because of codon bias Some organelles and a few cells have slight variations of the genetic code (e.g., mitochondria of animals, Mycoplasma, and Paramecium)
32
4.12 Transfer RNA tRNA and amino acid brought together by aminoacyl-tRNA synthetases
Acceptor stem 5′ 3′ phe 3′ A Acceptor end C TΨC loop C Acceptor end A 5′ C G Acceptor stem G C C G U G U A A U D loop U C A U D loop mA C G A C A G U A A mG C U C D G D C G U G U mC T C C G A G G Anticodon stem Ψ A U G G TΨC loop mG A mG G G C G C U A Anticodon stem Figure 4.34 Structure of a transfer RNA. mC G Y A A mC Y U A A A mG Anticodon A Anticodon 5′ 3′ mG U U C mRNA Anticodon loop Codon Figure 4.34
33
4.12 Transfer RNA Fidelity of recognition process between tRNA and aminoacyl-tRNA synthetase is critical (Figure 4.35) The “Second Genetic Code”?????? Incorrect amino acid could result in a faulty or nonfunctioning protein
34
Figure 4.35 Figure 4.35 Aminoacyl-tRNA synthetase. 5′ 3′ Amino acid
(valine) tRNA acceptor stem Uncharged tRNA specific for valine (tRNAVal) AMP C A Anticodon region Aminoacyl-tRNA synthetase for valine Linkage of valine to tRNAVal AMP Figure 4.35 Aminoacyl-tRNA synthetase. Valine Charged valyl tRNA, ready for protein synthesis Anticodon loop C A Figure 4.35
35
4.13 Protein Synthesis Polysomes: a complex formed by ribosomes simultaneously translating mRNA (Figure 4.37)
36
4.14 Protein Folding and Secretion
Once formed, a polypeptide folds to form a more stable structure. Secondary structure Interactions of the R groups force the molecule to twist and fold in a certain way (Figure 4.39) Tertiary structure Three-dimensional shape of polypeptide (Figure 4.40) Quaternary structure Number and types of polypeptides that make a protein
37
α-Helix β-Sheet Figure 4.40 A chain B chain Insulin Ribonuclease S S S
Figure 4.40 Tertiary structure of polypeptides. β-Sheet Insulin Ribonuclease Figure 4.40
38
4.14 Protein Folding and Secretion
Most polypeptides fold spontaneously into their active form Some require assistance from molecular chaperones or chaperonins for folding to occur (Figure 4.41) They only assist in the folding; they are not incorporated into protein Can also aid in refolding partially denatured proteins
39
DnaK aka Hsp70 DnaJ aka Hsp40 Figure 4.41 ATP ATP ADP
Improperly folded protein “client” protein DnaK DnaJ Properly folded (active) protein Transfer of improperly folded protein to GroEL/ES GroEL ATP Molecular chaperone ADP GroES Figure 4.41 The activity of molecular chaperones. DnaK aka Hsp70 DnaJ aka Hsp40 Properly folded (active) protein Figure 4.41
40
4.14 Protein Folding and Secretion
Signal sequences: found on proteins requiring transport from cell (Figure 4.42) 15–20 residues long Found at the beginning of the protein molecule Signal the cell's secretory system (Sec system) Prevent protein from completely folding
41
Figure 4.42 Cytoplasmic membrane SecA Periplasm Protein
Translational apparatus SecA Periplasm Protein Protein secreted into periplasm Ribosome Proteins with signal sequence mRNA Protein inserted into membrane Figure 4.42 Export of proteins via the major secretory system. Signal recognition particle Protein does not contain signal sequence. Membrane secretion system Figure 4.42
42
4.14 Protein Folding and Secretion
Secretion of folded proteins: the Tat system Proteins that fold in the cytoplasm are exported by a transport system distinct from Sec, called the Tat protein export system Iron–sulfur proteins Redox proteins
43
4.14 Protein Folding and Secretion
Secretion of proteins: types I through VI (Figure 4.43) All are a large complex of proteins that form channels through membranes Types II and V depend on Sec or Tat Types I, III, IV, and VI do not require Sec or Tat
44
From gram-negative bacterial cell:
Cytoplasmic membrane Outer membrane The injectisome traverses both the cytoplasmic and gram-negative outer membranes. Eukaryotic cytoplasmic membrane Protein, for example, a toxin Injectisome (type III secretion system) protein complex Figure 4.43 Secretion of molecules in gram-negative bacteria using the type III "injectisome" system. Figure 4.43
Similar presentations
© 2025 SlidePlayer.com. Inc.
All rights reserved.