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cell mol > Module 3 - Gene Expression Regulation > Flashcards

Module 3 - Gene Expression Regulation Flashcards

1
Q
  • using a gene to make a protein
  • the synthesis of the protein by the processes of transcription of DNA and translation of mRNA
  • may also include further processing of the protein after synthesis
A

gene expression

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2
Q

Gene expression is _________ to ensure that the correct proteins are made when and where they are needed.

A

regulated

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3
Q

When is gene expression regulated?

A

Regulation may occur at any point in the expression of a gene, from the start of the transcription phase of protein synthesis to the processing of a protein after synthesis occurs.

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4
Q

true or false

1.) all somatic cells within an organism contain the same DNA
2.) all cells within that organism express the same proteins

A
  1. True
  2. False
    within an organism, all somatic cells contain the same DNA but not all cells express the same protein
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5
Q

prokaryotic gene expression vs eukaryotic gene expression

A

Prokaryotic organisms:
- express the entire DNA they encode in every cell
- not necessarily all at the same time (only when they are needed)

Eukaryotic organisms
- express a subset of the DNA that is encoded in any given cell or expressed

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6
Q

in eukaryotic organism, the type and amount of protein is regulated by ________

A

controlling gene expression

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7
Q

To express a protein, the _____ is first transcribed into _______, which is then translated into ________.

A

DNA
RNA
proteins

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8
Q

In prokaryotic cells, transcription and translation occur_________ in ______ .
In eukaryotic cells, transcription occurs ________ and translation occurs in the _________

A

prokaryotic cells:
almost simultaneously
cytoplasm

eukaryotic cells:
transcription - nucleus
translation - cytoplasm

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9
Q

Gene expression in prokaryotes is mostly regulated at what level?

Whereas in eukaryotic cells, gene expression is regulated at the __________(5).

A

prokaryotic cells:
* transcriptional level (some epigenetic and post-translational regulation is also present)

eukaryotic cells:
* epigenetic
* transcriptional
* post-transcriptional
* translational
* post-translational levels

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10
Q

the mechanisms and systems that control the expression of genes

A

Gene Regulation

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11
Q

Gene expression is the overall process by which the information encoded in a ____ is converted into _________ (most commonly the__________).

A

gene
observable phenotype (most commonly the production of a protein)

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12
Q

Why regulate gene expression?
For the cell or organisms to: (3)

A
  • adjust to sudden changes
  • conserve energy
  • save resources
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13
Q

all of the mechanisms involved in regulating gene expression

A

gene control

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14
Q

gene control (2)

which the most common gene control

A
  • regulation of transcription (most common)
  • mechanisms influencing the processing, stabilization, and translation of mRNAs
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15
Q

provided a molecular basis for the connection between genotype and phenotype

A

central dogma

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16
Q

How is the flow of information along the molecular pathway regulated in the central dogma?

bacteria: gene regulation maintains internal flexibility, it _____________ in response to environmental changes

eukaryotic organisms: gene regulation brings about __________

A

bacteria: turns genes on and off
eukaryotes: cellular differentiation

  • Gene regulation and cellular differentiation are closely related because gene regulation is responsible for controlling the expression of genes that drive cellular differentiation
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17
Q

In considering gene regulation in both bacteria and eukaryotes, we must distinguish two DNA
sequences (2)

A
  • DNA sequences that are transcribed
  • DNA sequences that regulate the expression of other sequences
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18
Q

encode proteins that are used in metabolism or biosynthesis or that play a structural role in
the cell

A

Structural Genes (ex: lac operon)

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19
Q
  • genes whose products, either RNA or proteins interact with other sequences and affect the transcription or translation of those sequences
  • genes that bacteria and eukaryotes use to control the expression of many of their structural proteins
A

Regulatory Genes (ex: lacl gene)

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20
Q

the products of regulatory genes are

A

DNA-BINDING PROTEINS

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21
Q

a few genes (particularly those that encode essential cellular functions) that are expressed continually

A

Constitutive genes (ex: housekeeping gene)

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22
Q

DNA sequences that are not transcribed but affect the expression of genes. The function of the genome crucially involves regulatory sequences, such as enhancers and promoters.

A

Regulatory elements (ex: TATA box)

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23
Q

The regulation of gene expression can be: (2)

A
  • Positive control
  • Negative control
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24
Q

regulation of gene expression that includes mechanisms or processes that stimulate gene expression

A

Positive control

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25
Q

regulation of gene expression that includes processes that inhibit gene expression

A

Negative control

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26
Q

positive or negative control?

  1. Promoter-catabolite repression system
  2. Inducible lac system
  3. Repressible trp system
A
  1. Positive Control
    Promoter-catabolite repression system - the regulatory molecule (CRP-cAMP complex) enhances transcription

2-3. Negative control
Inducible lac system and Repressible trp system - in these two operator-repressor systems, the regulatory molecule (repressor) prevents transcription

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27
Q

Bacteria and eukaryotes use both positive and negative control mechanisms to regulate their genes. However, ____________ is more important in bacteria, whereas eukaryotes are more likely to use _________ mechanisms

A

negative (-) control
positive (+) control

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28
Q

can be controlled at any of a number of points along the molecular pathway from DNA to
protein, including :
* gene structure
* transcription
* mRNA processing
* RNA stability
* translation
* posttranslational modification.

A

Gene expression

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29
Q

These regulatory proteins generally have discrete functional parts called _______ (consisting of _____ amino acids; responsible for binding to DNA).

A

domains (60-90 amino acids)

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30
Q

DNA-Binding Proteins recognize and bind to specific DNA sequences or the ___________, typically _______ nucleotide pairs in length, and affect their __________.

A

cis-regulatory sequences
5–10
expression

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31
Q

DNA-binding proteins can be grouped into several distinct types on the basis of a characteristic structure
called a _________, found within the binding domain.

A

motif

32
Q

These motifs generally use either _______ or ______ to bind to the ______ groove of DNA.

A

α helices or β sheets
major groove

33
Q

DNA measurement

major grove
minor grove
1 helical turn
width

A

major grove: 12 Angstroms
minor grove: 6 Angstroms
1 helical turn: 34 Angstroms
width: 20 Angstroms

34
Q

what part of the DNA-binding proteins make the specific contacts with the DNA

A

amino acid side chains

35
Q

COMMON DNA-BINDING MOTIFS (5)

A

Helix-turn-helix
Zinc finger
Leucine zipper
Helix-loop-helix
Homeodomain

36
Q

Helix-turn-helix

Location:
Characteristics:
Binding Site in DNA:
Utilization:

A

Location: Bacterial regulatory proteins; related motifs in eukaryotic proteins

Characteristics: Two alpha helices

Binding Site in DNA: Major groove

Utilization: by binding to specific DNA sequences in the promoter regions of genes.

37
Q

Zinc finger

Location:
Characteristics:
Binding Site in DNA:
Utilization:

A

Location: Eukaryotic regulatory and other
proteins

Characteristics: Loop of amino acids with
zinc at base

Binding Site in DNA: Major groove

Utilization: sequence-specific DNA binding

38
Q

Leucine zipper

Location:
Characteristics:
Binding Site in DNA:
Utilization:

A

Location: Eukaryotic transcription factors

Characteristics: Loop of amino acids with
zinc at base

Binding Site in DNA: Two adjacent major
grooves

Utilization: protein-protein interactions and can stabilize the binding of transcription factors to DNA

39
Q

Helix-loop-helix

Location:
Characteristics:
Binding Site in DNA:
Utilization:

A

Location: Eukaryotic proteins

Characteristics: Two alpha helices separated by a loop of amino acids

Binding Site in DNA: Major grooves

Utilization: involved in dimerization and DNA binding

40
Q

Homeodomain

Location:
Characteristics:
Binding Site in DNA:
Utilization:

A

Location: Eukaryotic regulatory proteins
Characteristics: Three alpha helices
Binding Site in DNA: Major groove
Utilization: regulate developmental processes, specifying body patterns and cell differentiation

41
Q

example of helix-turn-helix proteins (4)

A

Tryptophan repressor
Lambda Cro
Lambda repressor fragment
CAP fragment

42
Q

__________ control genes at the transcriptional level - a gene is either transcribed or not

A

Prokaryotes

43
Q

Proteins that are needed for a specific function, or that are involved in the same biochemical pathway, are encoded together in blocks called

A

operons

44
Q

The operon: a segment of DNA that consists of the following: (3)

A

a) structural genes
b) promoter
c) operator

45
Q

DNA-dependent __________ binds the promoter region

A

RNA polymerase

46
Q
  • on/off switch;
  • region where the repressor binds to in response to external stimuli
A

Operator

47
Q

code for different proteins; all genes in the operon get transcribed from a ______ promoter

A

Structural Genes get transcribed from a single promoter

48
Q

In prokaryotic cells, three types of regulatory molecules (ginahimo sa regulatory genes) that can affect the expression of operons:

A
  • activators - increase the transcription
  • repressors - suppress the transcription
  • inducers - either activate or repress (depending on the needs of the cell and the availability of substrate)
49
Q

is an essential amino acid that E. coli can ingest from
the environment.
What type of regulatory molecule?
What operon siya mubind?
What are its five structural genes in sequential order?

A

Tryptophan, repressor, trp operon,
trpE, trpD, trpC, trpB, trpA

50
Q

__________ (1) is a transcriptional activator where it must bind to cAMP to activate transcription of the lac operon by RNA polymerase.

A

Catabolite Activator Protein (CAP) - Activator

51
Q

______ molecules bind to CAP and function as allosteric effectors by increasing CAP’s affinity to DNA.

A

cyclic AMP (cAMP) molecules

52
Q

When glucose levels fall, E. coli may use other sugars for fuel, but must transcribe new genes to do so. As glucose supplies become limited, _____ levels increase.

This cAMP binds to the _________, a positive regulator that binds to an operator region upstream of the genes required to use other sugar sources

A

cAMP
CAP protein

53
Q

Transcription of the _________ is carefully regulated so that its expression only occurs when glucose is limited and lactose is present to serve as an alternative fuel source.

What type of regulatory molecule?

A

lac operon
inducer:

  • operon off: lactose absent, repressor binds to operator
  • operon on: lactose present and binds to repressor
54
Q

Lac operon structural genes (3)

What is the regulatory gene of the lac operon where the repressor for the lac operon operator is transcribed?

A
  • lacZ (-> Beta-Galactosidase)
  • lacY(-> Permease)
  • lacA (-> Transacetylase)

lacI

55
Q

does the repressor binds and is there transcription of the lac operon when:

1.) Glu (+), CAP binds (-), Lac (-)
2.) Glu (+), CAP binds (-), Lac (+)
3.) Glu (-), CAP binds (+), Lac (-)
4.) Glu (-), CAP binds (+), Lac (+)

A

1.) repressor binds (+), no transcription
2.) repressor binds (-), some
3.) repressor binds (+), no
4.) repressor binds (-), yes

56
Q

In E. coli, the trp operon is on by default, while the lac operon is off. Why do you think this is the case?

A

The trp operon is ON by default to ensure the production of tryptophan when needed. In contrast, the lac operon is OFF by default to conserve energy and only activate lactose metabolism when glucose is limited.

57
Q

in ________ system, the substrate of a metabolic pathway (the inducer) interacts with a regulatory protein (the repressor) to render it incapable of binding to the operator, thus allowing transcription

A

inducible system

58
Q

in ________ system, the product of a metabolic pathway (the corepresssor) interacts with the regulatory protein to make it capable of binding to the operator, thus blocking the transcription

A

repressible system

59
Q

in ___________ system, the regulatory molecule functions by binding to the operator

A

inducible and repressible system (both kinds of system)

60
Q

Eukaryotic gene expression

  • is more complex than prokaryotic gene expression because the processes of transcription and translation are __________.
  • regulate gene expression at many different levels
  • begins with control of access to the DNA

This form of regulation, called _________, occurs even before transcription is initiated.

A

physically separated
epigenetic regulation

61
Q

eukaryotic epigenetic gene regulation (3)

A
  • regulate access to genes within chromosomes
  • transcription factors
  • post-transcriptional genes
62
Q

The __________ slide down the DNA to open that specific chromosomal region and allow for the transcriptional machinery (RNA polymerase) to initiate
transcription.

A

nucleosomes

63
Q

How the histone proteins move is dependent on signals found on both the histone proteins and on the DNA. These signals are _______ added to histone proteins and DNA that tell the histones if a chromosomal region should be open or closed

A

tags

64
Q

These tags are not permanent, but may be added or removed as needed. They are chemical modifications (__________, _______, or _________) that are attached to specific amino acids in the protein or to the nucleotides of the DNA. The tags do not alter the DNA base sequence, but they do alter how tightly wound the DNA is around the histone proteins.

A

phosphate, methyl, or acetyl groups

65
Q

Modifications to the histones and DNA affect ________ spacing

  • Nucleosomes can slide along DNA. When nucleosomes are spaced closely together (top), transcription factors cannot bind and gene expression is turned off.
  • When the nucleosomes are spaced far apart (bottom), the DNA is exposed. Transcription factors can bind, allowing gene expression to occur.
A

nucleosome

66
Q

are proteins that bind to the promoter sequence and other regulatory sequences to control the transcription of the target gene, in eukaryotic cells. RNA polymerase by itself cannot initiate transcription in eukaryotic cells.

A

transcription factors

Transcription factors must bind to the promoter region first and recruit RNA polymerase to the site for transcription to be established

67
Q

can bind to the promoter or enhancer regions and block transcription.

A

transcription repressors

68
Q

Post-transcriptional control can occur at any stage after transcription, including (3)

A

RNA splicing, nuclear shuttling, and RNA stability

69
Q

RNA is transported to the cytoplasm through
the

A

nuclear pore complex.

70
Q

RNA stability is controlled by___________ and __________ that bind to the 5’ UTR or the 3’ UTR of the RNA to increase or decrease RNA stability.

*Depending on the RBP, the stability can be increased or decreased significantly
* miRNAs always decrease stability and promote decay

A

RNA-binding proteins (RPBs) and microRNAs (miRNAs)

71
Q

As the _________ changes, the amount of time that
it is available for translation also changes.

A

stability

72
Q

Changing the status of the RNA or the protein itself can affect the amount of protein, the function of the protein, or how long it is found in the cell.
* To translate the protein, a protein initiator complex must assemble on the RNA.
* Once a protein has been synthesized, it can be modified (4).
* These post-translational modifications can greatly impact the stability, degradation, or function of the protein

A

phosphorylated, acetylated, methylated, or ubiquitinated

73
Q
  • Cancer-causing mutations most often occur in two types of regulatory genes, called
A

a) proto-oncogenes and b) tumorsuppressor genes

74
Q

are genes that normally help cells divide.

A

Proto-oncogenes

75
Q

are genes that normally slow down or stop cell division

A

Tumor suppressor genes

cell mol (9 decks)

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