Module 3 - Gene Expression Regulation Flashcards by Ateeya Cali

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

gene expression

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

regulated

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When is gene expression regulated?

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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true or false

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

True
False
within an organism, all somatic cells contain the same DNA but not all cells express the same protein

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prokaryotic gene expression vs eukaryotic gene expression

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

controlling gene expression

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

DNA
RNA
proteins

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

prokaryotic cells:
almost simultaneously
cytoplasm

eukaryotic cells:
transcription - nucleus
translation - cytoplasm

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Gene expression in prokaryotes is mostly regulated at what level?

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

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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the mechanisms and systems that control the expression of genes

Gene Regulation

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

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

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

adjust to sudden changes
conserve energy
save resources

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all of the mechanisms involved in regulating gene expression

gene control

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gene control (2)

which the most common gene control

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

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provided a molecular basis for the connection between genotype and phenotype

central dogma

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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 __________

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

DNA sequences that are transcribed
DNA sequences that regulate the expression of other sequences

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

Structural Genes (ex: lac operon)

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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

Regulatory Genes (ex: lacl gene)

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the products of regulatory genes are

DNA-BINDING PROTEINS

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

Constitutive genes (ex: housekeeping gene)

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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.

Regulatory elements (ex: TATA box)

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The regulation of gene expression can be: (2)

Positive control
Negative control

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

Positive control

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regulation of gene expression that includes processes that inhibit gene expression

Negative control

positive or negative control? 1. Promoter-catabolite repression system 2. Inducible lac system 3. Repressible trp system

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

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

negative (-) control positive (+) control

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.

Gene expression

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

domains (60-90 amino acids)

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

cis-regulatory sequences 5–10 expression

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

motif

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

α helices or β sheets major groove

DNA measurement major grove minor grove 1 helical turn width

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

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

amino acid side chains

COMMON DNA-BINDING MOTIFS (5)

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

Helix-turn-helix Location: Characteristics: Binding Site in DNA: Utilization:

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.

Zinc finger Location: Characteristics: Binding Site in DNA: Utilization:

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

Leucine zipper Location: Characteristics: Binding Site in DNA: Utilization:

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

Helix-loop-helix Location: Characteristics: Binding Site in DNA: Utilization:

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

Homeodomain Location: Characteristics: Binding Site in DNA: Utilization:

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

example of helix-turn-helix proteins (4)

Tryptophan repressor Lambda Cro Lambda repressor fragment CAP fragment

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

Prokaryotes

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

operons

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

a) structural genes b) promoter c) operator

DNA-dependent __________ binds the promoter region

RNA polymerase

- on/off switch; - region where the repressor binds to in response to external stimuli

Operator

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

**Structural Genes** get transcribed from a **single** promoter

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

* **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)

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?

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

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

Catabolite Activator Protein (CAP) - Activator

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

cyclic AMP (cAMP) molecules

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

cAMP CAP protein

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?

lac operon inducer: * operon off: lactose absent, repressor binds to operator * operon on: lactose present and binds to repressor

Lac operon structural genes (3) What is the regulatory gene of the lac operon where the repressor for the lac operon operator is transcribed?

* lacZ (-> Beta-Galactosidase) * lacY(-> Permease) * lacA (-> Transacetylase) lacI

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 (+)

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

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

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*.

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**

inducible system

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

repressible system

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

inducible and repressible system (both kinds of system)

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.

physically separated epigenetic regulation

eukaryotic epigenetic gene regulation (3)

* regulate access to genes within chromosomes * transcription factors * post-transcriptional genes

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

nucleosomes

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