Control Mechanisms

1. Control Mechanisms • Gene regulation involvesturning on or off specific genes depending on the needs of the organism. • Transcription factors turn on genes by binding to DNA and helping RNA polymerase bind. • NOTE: Housekeeping genesare always needed and are constantly being transcribed and translated.

2. 5.5 Control Mechanisms • Every living cell has the ability to respond to its environment by changing the kinds and amounts of polypeptides it produces. Cells have developed methods by which they can control the transcription and translation of genes, depending on their need.

3. Gene regulation can occur at different levels: • Transcriptional: how fast/slow transcription occurs • Posttranscriptional: how fast/slow RNA processing occurs • Translational: how fast/slow mRNA is transcribed • Posttranslational: how fast/slow the protein becomes active and functional

4. Operons • Operons = are clusters of genes under the control of one promoter and one operator ex lac operon, trp operon

5. oForm of control only used in bacteria • oIn bacteria such as E.coli found in the digestive system of mamals, β-galactosidase is the enzyme responsible for breaking down lactose (enzyme is not always required) • oβ-galactosidase is part of an operon • olacl protein binds to operon blocking transcription • oin the presence of lactose a repressorprotein (lacl protein) normally bound to operon leaves and binds to lactose  transcription of the lac operon no longer blocked (no enzymes are made)  see fig. 2 p. 256 • oWhy? When there is no milk, no enzyme is needed

6. E. coli bacterial cells that are in the intestines of mammals can use the energy supplied by lactose in order to grow by breaking the bonds between the two sugars. • -galactosidase is the enzyme used to break down lactose. But bacteria only produce it when they need to, so they must regulate the production of -galactosidase using a negative control system. •    The gene for -galactosidase is part of an operon (cluster of genes under the control of one promotor and one operator) •  The lac operon has three genes that code for protein involved in the breakdown of lactose: lacZ, lacY, and lacA.

7. The lacZ gene encodes the enzyme -galactosidase •  The lacY gene encodes the -galactosidase permease (that causes lactose to permeate the cell membrane and enter the cell) • The lacA encodes a transacetylase (we don’t know what it does though) • The LacI protein is a repressor protein that blocks the transcription of the -galactosidase by binding to the lactose operator and getting in the way of the RNA polymerase

8. If lactose is introduced, the roadblock (LacI protein) must be removed. The presence of lactose itself removes the protein and is known as the signal molecule or the inducer. •   Lactose binds to the LacI protein, which changes the conformation of the protein and it can no longer stay bound to the operator region of the lac operon. The complex falls off the DNA and it allows the RNA polymerase to proceed and transcribe the lac operon.

9. The trp Operon • ·Works in the opposite manner to the lac operon • ·tryptophan is an amino acid used by bacteria to produce proteins, when available in its environment bacteria stop producing tryptophan and absorb it from its environment • ·operon acitivity is inhibited when the concentration of tryptophan in the environment increases  tryptophan binds to operator region of operon  see fig. 3, p. 257

10. The trp operon is another example of coordinated regulation. •   The trp operon is repressed when high levels of tryptophan are present. • The trp operon has five genes that code for five polypeptides that make enzymes needed to make tryptophan. • When tryptophan levels are high, the tryptophan molecule binds to the repressor protein, altering its shape and binds with the trp operator. •   Because tryptophan is needed itself to inactivate the trp operon, it is called a corepressor.

11. Negative Gene Regulation in the lac Operon

12. Co-Repression in the trp Operon

13. Summary lac Operon • Transcription induced when high levels of lactose present. trp Operon • Transcription repressed when high levels of tryptophan present.

14. 5.6: Mutations • Inherited errors made in the DNA sequence.

15. Mutations Can be • 1. Negative: genetic disorders/diseases • 2. Positive: natural selection (ex. Large human brain size • 3. Have no effect

16. Types of Mutations There are 7 types we are going to review.

17. 1. Silent • has no effect • occur in noncoding regions (introns) • base change codes for the original amino acid

18. 2. Missense • base change leads to a different amino acid • ex. Sickle cell anemia

19. 3. Nonsense • base change causes a stop codon to replace an amino acid • these are often lethal to the cell because the required protein is not produced Animation Quiz 3 - Mutation by Base Substitution

20. 4. Deletion • one or more nucleotides are removed, results in defective protein

21. 5. Insertion • inserting extra nucleotides results in different amino acids being translated Animation Quiz 4 - Addition and Deletion Mutations

22. 6. Translocation • involves large segments of DNA (chromosomes) • groups of base pairs relocate from one part of the genome to another • a part of one chromosome breaks and is released while the same thing happens to another (usually non-homologous chromosome) and the two parts exchange places. • Some fragments of DNA called transposable elements consistently move from one location to another. If they land within a coding region, they will disrupt transcription

23. Translocation

24. 7. Inversion • a chromosomal segment that has reversed its orientation in the chromosome. • No loss of genetic info, but genes may be disrupted.

25. Key Points: • Missense and Silent mutations arise from substitution of one base pair for another known as point mutation. • Insertion and Deletion cause frameshift mutations (reading frame is changed). • Translocation and Inversion involve the whole chromosome.

26. Causes 1. Spontaneous:simple errors 2. Induced: caused by mutagenic agents such as UV radiation, cosmic rays, x-rays and chemicals

28. 5.7: Endosymbiosis • Protein Synthesis: Prokaryotes vs. Eukaryotes

29. Since prokaryotes do not possess a nuclear membrane, trancription and translation can be coupled.

30. Endosymbiotic Relationships between Organelles and Cells • Mitochondria resemble prokaryotic cells in the following way: •  1.  Both contain circular DNA that is not enclosed in a nucleus. • 2. Sequence of DNA is similar. •  3.  Both divide by fission. •  4.  Mitochondria possess their own process of DNA replication and protein synthesis.

31. Differences between Eukaryotes and Prokaryotes • 1.    Prokaryotes do not posses a nuclear membrane. Coupled transcription-translation • 2.    Prokaryotes do not contain introns (non-coding regions) • Prokaryotes, ribosome recognizes a unique protein-rich base known as the Shine-Dalgarno sequence at the start of mRNA. Eukaryotes, ribosomes recognize 5’ cap.

32. Differences between Eukaryotes and Prokaryotes • 5.    Eukaryotic ribosomes are larger. • 6.    Methionine is the first amino acid in both Prokaryotes and Eukaryotes. In prokaryotes it is tagges with a formyl group. • 7.  Eukaryotes do not have operons. • 8   Prokaryotic genome is circular, Eukaryotic genome is organized in chromosomes.

33. 5.8: Gene Organization and Chromosome Structure