Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIMM 120 > Chapter 8 > Flashcards

Chapter 8 Flashcards

1
Q

What is gene expression

A

Gene expression is the production of a gene product, usually transcription (mRNA) and translation (protein)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are most of the proteins encoded

A

Enzymes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are constitutive proteins

A

They are proteins that are needed at the same level at all times, these genes are continuously expressed (housekeeping gene ex. genes for the ribosomes)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is gene regulation

A

Genes can be turned on or off, they coordinate cellular activities and conserves energy and resources

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is a structural gene

A

It is the open reading frame that codes for the transcript, sequences between the start/stop codon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is the shine-dalgarno sequence

A

The sequence that serves as the ribosome-binding site, it is JUST downstream of the start site for transcription and JUST upstream of the translation start codon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What kind of processing does the RNA undergo in bacteria

A

None, there is no splicing, poly A tail or cappingg

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are the two major levels of regulation in the cell

A

Control activity of preexisting enzymes and control amount of an enzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Describe control activity of preexisting enzymes in regulation

A

It is very rapid, post translational regulation ex. feedback inhibition and covalent modification

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Describe control amount of an enzyme in regulationn

A

It is very slow, regulates transcription and regulates translation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What are transcription factors

A

Regulation of transcription typically requires proteins that can bind to DNA known as transcription factors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What regulates transcription factors

A

They can be regulated by: their own synthesis, allosterically by small molecules (metabolites) and by covalent modification (phosphorylation)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are the two ways transcription factors can regulate transcription

A

Negatively (repressors) or positively (activators)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How long is the half-life of mRNA transcripts

A

They have short half-lifes, only a few minutes. This prevents the production of unneeded proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How do DNA-binding proteins interact with DNA

A

They interact with DNA in a sequence-specific manner, the specificity is provided by amino acid side chains interacting with the DNA bases (on the major groove)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are homodimeric proteins

A

Most transcription factors are homodimeric proteins: proteins that are composed of two identical polypeptides, these protein dimers interact with inverted repeats on DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

How do homodimeric proteins interact with DNA

A

Each of the polypeptides binds to one side of the inverted repeat on the DNA, this increases specificity of just a single protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What are inverted repeats

A

They are sequences on opposite strands and sides of the DNA strands that “move” towards each other

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is one class of protein domain that is critical for binding to DNA

A

Helix-turn-helix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Describe the structure of the Helix-turn-helix protein domain

A

It has two subunits: one is the stabalizing helix and one is the recognition helix. There is also a strand “turn” that connects the subunits

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What are the activities of DNA-binding proteins

A

They may catalyze a specific reaction on the DNA molecule: transcription by RNA polymerase or transposition by transposase.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What are repressors

A

DNA binding proteins that block transcription (negative regulation)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What are activators

A

DNA binding proteins that stimulate transcription (positive regulation)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What regulates the activities of DNA binding proteins

A

The presence of absence of specific small molecules (metabolites or from environment) and intrecellular regulatory signals resulting in covalent modification, sequestration, o degradation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
What are are two methods of negative control of transcription
Repression and Induction
26
What does negative control of transcription mean
A regulatory mechanism that blocks/stops transcription and involves a repressor DNA-binding protein
27
What is repression
Preventing the synthesis of an enzyme in response to a signal. Typically affects ANABOLIC enzymes
28
What are two examples of anabolic enzymes
Arginine and tryptophan BIOSYNTHESIS
29
How does repression work
Enzymes for arginine biosynthesis are normally turned on. But if arginine is added to the cell culture, the bacterial cell can get arginine from the environment and the enzymes for arginine biosynthesis stop being made because the cell doesn't need too much arginine
30
Describe the regulatory proteins that are required in repression
The regulatory proteins themselves need to be made. The regulatory gene is a constitutive gene, it constantly produces a small amount of this DNA binding protein, the cell is always ready to turn the operon off but can only turn the operon off if there is a lot of tryptophan available
31
What is induction
The production of an enzyme in response to a signal. Typically affects CATABOLIC enzymes, these enzymes are only synthesized when they are needed
32
What is an example of a catabolic enzyme
In the lac operon
33
How does induction work
It is still considered negative regulation because it involves a repressor protein. First a cell is not making lactase because the genes that encode for it are repressed. If a lot of lactose is suddenly present in the environment, the lactase enzymes will increase. The repressor protein that is sitting on top of the genes that code for lactase will be induced and leave
34
What are corepressors
Substance that stimulates repressor function to repress enzyme synthesis. The addition of corepressors activate a repressor to turn off transcription
35
What are inducers
Substance that blocks repressor function and induces enzyme synthesis. The addition of an inducer inactivates the repressor transcription factor to turn on transcription
36
What are effectors
The collective term for inducer and corepressor molecules. They affect transcription indirectly by binding allosterically to specific transcription factor proteins. Ex. repressor-corepressor blocks transcription
37
What is an operon
A linear cluster of genes whose expression is under the control of a single OPERATOR sequence
38
Where it the operator located in relation to the promoter on the DNA
The operator is located downsstream of the promoter
39
How is transcription blocked
Transcription is physically blocked when repressor binds to operator
40
What is positive control
A regulator protein that activates the binding of RNA polymerase to DNA
41
Describe Maltose catabolism in E.coli
The maltose activator protein cannot bind to DNA unless it first binds to maltose, it is going to activate transcription. If maltose is present, its going to make the activator protein bind DNA and stimulate transcription.
42
Where do activator proteins bind
The activator proteins bind to certain DNA sequences called the activator binding sites, NOT on the operator
43
How do activators promote transcription
The gene sequence may have a promoter that the RNA polymerase can bind to but it kind of sucks. But near the promoter is an activator binding site. The activator protein coupled with an inducer can bind to the activator binding site and interacts with the RNA polymerase to recognize this promoter region more effectively
44
What happens with the activator binding site is far away from the promoter
DNA looping is required, this is possible due to the flexibility of the DNA
45
What is a regulon
Multiple operons that are controlled by the same regulatory protein ex. maltose. In the maltose regulon, all the operons are regulated in the same way
46
Why and how do prokaryotes regulate cellular metabolism
In response to environmental fluctuations. Can regulate cellular metabolism in response to external signals that are perceived by TF proteins and signal transductrion
47
Describe how external signals are usually perceived by TF proteins
Signals can be small molecules such as nutrients or they can be physical conditions such as temperature or light
48
What is signal transduction
External signal is detected by a sensor protein and a signal is then transmitted to regulatory machinery inside the cell (Two-component regulatory system)
49
What are the two proteins that make up the two-component regulatory system
Sensor kinase and response regulator
50
Describe the sensor kinase
Is in the cytoplasmic membrane, it detects environment signal and autophosphorylates.
51
What does the kinase do in the sensor kinase
The kinase adds the phosphate group to itself, usually from ATP
52
Describe the response regulator
In the cytoplasm, DNA-binding protein that regulates transcription. It is activated by the phophostransfer from the sensor kinase. Without the phosphate it is inactive
53
How do you stop the signalling in this signalling system
Desphosphorylation termiantes this signal and this can be carried out by phosphatase which removes the phosphate group
54
What does an activated response regulator do
Once its phosphorylated, it changes shape, and can bind to DNA to repress transcription. These genes can be turned back on again with phosphatase which will remove the phosphate so you can get back to the starting condition
55
What is Quorum sensing
A mechanism by which bacteria assess their population density
56
What does quorum sensing ensure
It ensures that a sufficient number of cells are present before initiating a response that requires a large cell density
57
What are some examples of quorum sensing responses
Light production by symbiotic bacteria, toxin production by pathogenic bacteria, P aeurginose switch from free living single cells to growing as a biofilm in lung, and virulence factors of staphylococcus aureus
58
What is an autoinducer
Each species of bacteria that does quorum sensing produces a specific autoinducer molecule. Most can diffuse freely out of cell, will reach high concentrations inside cell only if many cells are nearby, and binds to specific activator protein and triggers transcription of specific genes
59
What was the first autoinducer indentified
AHL - acyl homoserince lactone
60
What was the first quorum sensing discovered
Quorum sensing first discovered as mechanism regulating light production in bacteria. Establishes symbiosis with various marine animals, such as the squid.
61
What is the lux operon
The lux operon encodes enzymes for bioluminescence
62
Describe the mechanism of quorum sensing
All the species of bacteria will produce AHL molecules. When enough AHL molecules enter a cell (when there is high cell density) the AHL will bind to an activator protein and regulate gene expression on the chromosome. It will create quorum-specific proteins and make AHL synthase, which will make more AHLs
63
Describe endospore formation of Bacillus
There are 2 cell types: vegetative cells and endospores. It is controlled by 4 sigma factors and transcriptional factors. This is triggered by adverse external conditions
64
Describe the process of endospore formation
External signals for adverse conditions causes a cascade of sigma factors, each directing the expression of a different regulon of genes required for a particular stage of development
65
What are regulatory RNA molecules
They exert their effects by base pairing with mRNA. Their double-stranded region prevents translation of mRNA
66
What are antisense RNAs
Small RNAs that are about 100 nucleotides (regulatory RNA molecules). Transcription of the antisense RNA is upregulated when its target genes need to be turned off
67
What are riboswitches
RNA domains in an mRNA molecule that can bind a small molecule (metabolite) to control translation. Located at the 5' end of the mRNA, binding results from folding of RNA into 3D strucutre, similar to protein recognizing a substrate. Riboswitch is analogous to negative control.
68
Describe the mechanism of the riboswitch
Normally the RNA will have a secondary structure and a flat shine-dalgarno sequence for ribosome biding and translation will proceed. When a riboswitch binds, it creates a loop secondary structure upstream of the shine-dalgarno sequence and the shine-dalgarno sequence will be moved into another secondary structure loop and translation can't occur

BIMM 120 (17 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions