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Biology 2112 Study Guide Examination 4
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Biology 2112 Study Guide Examination 4
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STUDY GUIDE - EXAMINATION 4Lecture 24 - Bacterial Gene Regulation
1) Bacteria respond to changes in their environments, such as nutrient availability, by regulating their
metabolic pathways. Describe two mechanisms that bacteria use in order to adapt to environmental
changes. Include in your answer which mechanism is a short-term or long-term adaptation.
- 1. cells can adjust the activity of enzymes already present (short term).
2. cells can adjust the production level of certain enzymes; they can regulate the expression of
the genes encoding the enzyme (long term).
2)
a. What is an operon and what is the advantage to this gene structure? (Pg. 365, paragraph 1,
sentence 1; pg. 364, column 2, paragraph 2, sentence 1)
- A unit of genetic function found in bacteria and phages, consisting of a promoter, and operator,
and a coordinately regulated cluster of genes whose products function in a common pathway;
- A key advantage of grouping genes of related functions into one transcription unit is that a single
"on-off" switch can control the whole closet of functionally related genes.
b. What is an operator sequence and where is it located within an operon? (Pg. 364, column 2,
paragraph 2, boldface)
- The on-off switch is a segment of DNA called an operator; its location and name suits its function:
positioned within the operate or, in some cases, between the promoter and the enzyme-coding
genes, the operator controls the access of RNA polymerase to the genes.
3) In terms of an operon, what is a repressor and corepressor, and how do these two factors function?
(Pg. 365, boldface)
- Repressor: binds to the operator and blocks attachment of RNA polymerase to the promoter,
preventing transcription of the genes.
- Corepressor: a small molecule that cooperates with a repressor protein to switch an operon off.
4) What is the difference between repressible and inducible operons? (Pg. 366, paragraph 1, sentences
1-2)
- Repressible operon: transcription is usually on but can be inhibited (repressed) when a specific
small molecule binds allosterically to a regulatory protein
- Inducible operon: usually off but can be stimulated (induced) to be on when a specific small
molecule interacts with a different regulatory protein
5) What is the role of an inducer in an operon? (Pg. 366, boldface and Fig. 18.4b)
- A specific small molecule that inactivates the repressor.
6) What is the difference between repressible and inducible enzymes and in what pathways do these
types of enzymes usually operate? (Pg. 366, final paragraph)
- Inducible enzymes: catabolic pathways; produce the appropriate enzymes only when the
nutrient is available, the cell avoids wasting energy and precursors making proteins that are not
needed.
- Repressible enzymes: anabolic pathways; suspend production of an end product when it is
already present in sufficient quantity, the cell can allocate its organic precursors and energy for
other uses.
,7) What is the difference between negative and positive gene regulation? (Pg. 367, paragraph 2)
- Negative: the operons are switched off by the active form of their respective repressor protein
- Positive: a regulatory protein interacts directly with the genome to switch transcription on
8) How does the catabolite activator protein (CAP) affect transcription of the lac operon? (Pg. 367,
paragraph 4, sentences 3-7 and Fig. 18.5)
- The regulatory protein, called cAMP receptor protein (CRP), is an activator, a protein that binds to
DNA and stimulates transcription of a gene. When cAMP binds to this regulatory protein, CRP
assumes its active shape and can attach to a specific site at the upstream end of the lac
promoter. This attachment increases the affinity of RNA polymerase for the lac promoter, which is
actually rather low even when no lac repressor is bound to the operator. By facilitating the binding
of RNA polymerase to the promoter and thereby increasing the rate of transcription of the lac
operon, the attachment of CRP to the promoter directly stimulates gene expression. Therefore,
this mechanism qualifies as positive regulation.
9) Describe the dual control of the lac operon. (Pg. 367, paragraph 5, sentences 3-4)
- If the amount of glucose in the cell increases, the cAMP concentration falls, and without cAMP,
CRP (cAMP receptor protein) detaches from the lac operon. Because CRP is inactive, RNA
polymerase binds less efficiently to the promoter, and transcription of the lac operon proceeds
only at a low level, even when lactose is present. Thus, the lac operon is under dual control:
negative control by the lac repressor and positive control by CRP. The state of the lac repressor
(with allolactose bound or without it) determines whether or not transcription of the lac operon's
genes occurs at all; the state of CRP (with bound cAMP or without it) control the rat of
transcription if the operon is repressor-free.
10) What is the function of the CRISPR-Cas system in bacterial cells? (Pg. 402, paragraph 3 and figure
19.7)
- 1. Infection by a phage triggers transcription of the CRISPR region of the bacterial DNA. The
region consists of DNA from phages that previously infected the cell, separated by repeats.
2. The RNA transcript is processed into short RNA strands. Here we focus on RNA that is
complementary to the DNA of the invading phage.
3. Each short RNA strand binds to a Cas protein, forming a complex.
4. Complementary RNA binds to DNA from the invading phage. The Cas protein then cut the
phage DNA.
5. After being cut, the entire phage DNA molecule is degraded and can no longer be replicated.
Lecture 25 - Genome Organization and Eukaryotic Gene Regulation
1) How does differential gene expression relate to cellular differentiation? (Pg. 368, paragraph 2,
sentences 3, 5-6)
- Almost all cells in a multicellular organism contain an identical genome. A subset of genes
expressed in each cell type; some of these are "housekeeping" genes, expressed by many cell
types, while others are unique to that cell type. They uniquely expressed genes allow these cells
to carry out specific functions.
, 2) List the nine levels where gene expression is regulated. (Pg. 368, Fig. 18.6)
- 1. Chromatin modification: DNA unpacking
2. transcription
3. RNA processing
4. transport to cytoplasm
5. translation
6. degradation of mRNA
7. protein processing
8. degradation of protein
9. transport to cellular destination
3) Chromosomal DNA interacts with special DNA binding proteins to achieve four levels of “packing”. (Pg.
330-331, Fig. 16.22)
a. The first level of packing is the nucleosome. Describe the nucleosome. Include in your answer
how components of the nucleosome interact, the size of the nucleosome, and how much DNA it
contains. (Lecture notes)
- (10nm) Nucleosomes: are the basic unit of DNA packing; the "string" between beads is called
linker DNA. Nucleosomes consist of DNA wound twice around a protein core of eight histones,
two each of the main histone types. The amino acid of each histone extends outwards from the
nucleosome.
b. How does Histone HI establish the second level of chromatin packing? What is the size of the
fiber? (Pg. 331)
- The second level of packing is the coiling of beads in a helical structure called the 30 nm fiber
that is found in both interphase chromatin and mitotic chromosomes.
c. Describe the third level of chromatin packing. Include in your answer how this level of chromatin
structure is associated with transcriptional activity. (Pg. 331; Pg. 332, paragraph 2, sentences
4-5)
- Although an interphase chromosome lacks an obvious scaffold, its looped domains appear to be
attached to the nuclear lamina, on the inside of the nuclear envelope, and perhaps also to fibers
of the nuclear matrix. These attachments may help organize regions of chromatin where genes
are active.
d. When does chromatin develop the fourth level of packing and what is the size of the fibre? (Pg.
331, Figure 16.22)
- The final packing occurs when the fiber is organized in loops, scaffolds and domains then give a
final packing ratio of about 100 in interphase chromosomes and about 10,000 in mitotic
chromosomes. (1400nm)
4) What is the difference between euchromatin and heterochromatin, and where do you find them along
the length of a chromosome? (Pg. 332, paragraph 3)
- Even during interphase, the centromeres and telomeres of chromosomes, as well as other
chromosomal regions in some cells, exist in a highly condensed state similar to that seen in a
metaphase chromosome. This type of interphase chromatin, visible as irregular clumps with a
light microscope, is called HETEROCHROMATIN, to distinguish it from the less compacted, more
dispersed EUCHROMATIN (true chromatin).
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