BIO230H1 Lecture Notes - Lecture 2: T-Cell Lymphoma, Lambda Phage, Histone H2A

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When bound to dna, the activator protein promotes transcription. You cant just consider the protein, you also have to consider the ligand. When bound to dna, the repressor protein prevents transcription. If the ligand is present, you will take it off the dna and it cant prevent transcription. Bottom left: when bound to dna, the repressor protein pvents transcription, but here the ligand it can bind to dna and it can prevent gene transcription. Top right: when bound to dna, the activator protein allows transctiptin and since the ligand is present, it (cid:272)a(cid:374)t (cid:271)i(cid:374)d to d(cid:374)a a(cid:374)d it does(cid:374)"t a(cid:272)ti(cid:448)ate ge(cid:374)e tra(cid:374)s(cid:272)riptio(cid:374). Botto(cid:373) right: with the liga(cid:374)d, the protei(cid:374) can bind to dna and it allows gene transcription. Not all proteins have the helix turn helix shape, but fi you have it it means you bind in the major groove. Helix turn helix pattern is a common dna binding pattern in proteins. All of these poritions will influence gene transcription.

Related Questions

A transcription factor G can act as either a repressor or an activator of operon M, depending on its conformational state.

In one conformational state, transcription factor G binds site 1 in the promoter of operon M. When bound to site 1, it is an activator of operon M transcription. Factor G cannot bind to site 1 if ligand X is bound to it.

When factor G binds to ligand X, factor G undergoes a conformational change such that it now binds site 2 in the promoter and represses operon M. Because of the way in which it acts, ligand X would be called a(n) ____.

Imagine that there is a mutation in the gene that encodes transcription factor G such that operon M is always transcribed.

Which of these mutations in the gene that encodes transcription factor G is consistent with that outcome?

More than one answer may be correct.

'The mutation changes transcription factor G such that it ___'

cannot bind site 1

cannot bind site 2

cannot bind to ligand X

cannot dissociate from ligand X once it has bound

Continuing with the system in Questions 4 and 5, imagine that you are now analyzing mutations in the promoter of operon M. If site 1 is mutated such that factor G cannot bind, operon M will never be ____

repressed

activated

If site 2 is mutated such that factor G cannot bind, operon M will never be ____

repressed

activated

Still on system described in Q4,5,6,7. If there is a mutation in the DNA encoding biosynthesis genes such that ligand X cannot be made, operon M will never be ___

repressed

activated

QUESTION 10

If you can drink milk as an adult, it means that you have inherited a mutation in the promoter of your lactase gene (the gene that encodes the enzyme you need to break down lactose). Predict the effect of this mutation:

		The mutation changes the number of domains in the enzyme, which makes it work more efficiently
		The mutation changes the amino acid sequence of the lactase protein
		The mutation increases the number of copies of the lactase gene that will be found in your genome
		The mutation changes whether the lactase sequence is found in an intron or exon
		The mutation affects the expression of the lactase gene

1.2 points

QUESTION 11

A competitive inhibitor is decreasing the activity of an enzyme. Predict the effect of adding more substrate to the reaction.

		The substrate will increase the reaction rate by binding to the allosteric site
		The substrate will increase the reaction rate by competing with the inhibitor for the active site
		The reaction rate will not change unless the inhibitor can be removed
		The enzyme adjusts its shape so that the substrate, but NOT the competitive inhibitor, can bind
		The substrate will bind to the competitive inhibitor and block its ability to bind to the enzyme

1.2 points

QUESTION 12

What determines where in the genome a transcription regulator will bind?

		Transcription regulators bind to the 5' UTR region of a gene
		Regulators bind via complementary base-pairing to certain DNA molecules
		Covalent bonds form between the transcription regulator and the atoms of the DNA backbone
		Every eukaryotic gene has a different transcription regulator that will bind to the 5' end of the gene
		Transcription regulators bind to specific DNA sequences via multiple weak non-covalent interactions

1.2 points

QUESTION 13

What is the basic premise of cell theory?

		DNA -> RNA -> protein
		All cells arise from pre-existing cells
		DNA provides the complete instructions to create a cell
		The identity of a cell is determined through gene expression patterns
		All cells contain the same four basic macromolecules

1.2 points

QUESTION 14

What is the benefit of using BOTH the lac activator and the lac repressor to control gene expression?

		Using both an activator and repressor enables cells to more accurately determine the amount of lactose available in the environment
		Enzymes to digest lactose are only made when energy is low and lactose is available
		The activator can override the inhibition of the lac operon by the repressor
		The repressor can control the enhancer, while the activator can control the promoter
		When neither the lac activator or repressor is present, expression of the lac operon is too high

1.2 points

QUESTION 15

What is the histone code used for?

		Phosphorylation and acetylation of DNA affect its ability to be compacted
		Changes to the sequence of DNA change whether DNA will wrap around histone proteins
		Covalent modifications of histones affect the ability of the transcription initiation complex to form
		Histones provide the codon sequences needed for translation to occur
		The histone code affects which amino acids will get added to a polypeptide

I. Signaling cascades (4 pts)

1. Which of the following is an example of a signaling cascade?

A. Binding of lactose to the lac repressor

B. Binding of the lac repressor to the lac operon

C. The series of proteolytic digests that occur during clotting

D. The Collins Toggle Switch

2. Why is it important that signaling cascades have negative feedback loops?

II. Metabolism (4 pts)

1. What is a benefit of a negative feedback allosteric regulator?

A. It prevents starting materials from being unnecessarily consumed.

B. It regulated metabolism without requiring new protein synthesis.

C. It can be rapidly reversed as conditions change.

D. All of the above.

2. How is a metabolic cycle, like the citric cycle, distinct from a metabolic pathway, like glycolysis?

III. Transcription (4 pts)

1. Transcription factors, repressors, and activators are examples of proteins that _________.

A. randomly activate RNA polymerases.

B. bind specific DNA sequences.

C. bind specific rRNA sequences.

D. are found in the lysosome.

2. The trp operon is attenuated by a stem-loop structure that can form near RNA polymerase. The RNA sequencing encoding the stem loop is:

5â-AUACCCAGCCCGCCUAAUGAGCGGGCUU-3â

The stem loop is composed of 7 nucleotides which perfectly base pair. Indicate the two halves of the stem loop on the sequence above.

IV. DNA replication/repair/genome editing (4 pts)

1. What is a consequence of the need for RNA primers during DNA replication?

A. Linear chromosomes gradually shorten each cell division.

B. Transcription factors often trigger DNA replication.

C. RNA primers are not actually needed for DNA replication.

D. Lagging strands can be avoided.

2. CRISPR-mediated genome editing has gene-specific components: an sgRNA, and a double-stranded repair template. Describe the role of the sgRNA in directing genome editing.

V. Genetic circuits (4 pts)

1. Which statement best describes the mechanism of the toggle switch?

A. Inducers must be continuously applied to maintain one of two states.

B. Competing repressors keep the cell in one of two transcriptional states.

C. An activator and a repressor keep the cell in one of two states.

D. A pair of repressors cause the cell to oscillate between two states without input.

2. How is bistability achieved by the Collins toggle switch?

BIO230H1 Lecture Notes - Lecture 2: T-Cell Lymphoma, Lambda Phage, Histone H2A

BIO230H1 Full Course Notes

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