Exam 3 Flashcards by Justin Arthurs

T/F Regulatory Proteins bind to DNA to control transcription rate

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What are the two types of regulatory proteins?

Activators and Repressors

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How do effector molecules function to control transcription rate?

They bind to the regulatory proteins to cause a conformational change which affects transcription rate

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What are the types of effector molecules?

Inducers

Corepressor

Inhibitor

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What are inducible genes?

Genes that are regulated by inducers

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How do inducers function?

Bind either to a repressor to DEACTIVATE it or to an activator to ACTIVATE it more

— INCREASE transcription —

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How does a corepressor function?

Binds to a repressor protein which causes the protein to bind to DNA

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How does an inhibitor function?

Binds to an activator protein and PREVENTS the protein from binding to the DNA

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What are repressible genes?

Genes regulated by Corepressors or Inhibitors

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Describe the phenomenon of Enzyme Adaptation

Occurs when a particular enzyme appears only after the cell has been exposed to the substrate of that enzyme

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What is an Operon?

A group of two or more genes transcribed from ONE promoter

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What is a polycistronic mRNA?

An mRNA that encodes for 2 or more gene products (carries 2 or more gene sequences)

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The lac operon is regulated by a (activator/repressor/activaor and repressor) protein

Activator and Repressor

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Where does the lac repressor protein bind?

The lac operator site

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Describe how allolactose influences the ability of lac repressor to bind to the operator site.

If allolactose is present, it induces a conformational change which prevents the lac repressor from binding to the operator site

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If allolactose levels are high, transcription of the lac operon will (occur/not occur)

Occur

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The phenomenon in which the presence of allolactose influences the ability of lac repressor to bind to the lac operator site is an example of what type of regulation?

Allosteric

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T/F The presence of lactose in the environment leads to the production of allolactose

True

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How does the presence of glucose affect the lac operon?

Presence of glucose leads to repression of the lac operon because cAMP levels are low

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The lac operon has 3 operator sites. Describe how binding to the operator sites by lac repressor influences lac operon repression

The lac repressor must bind to Operator Site 1 AND to EITHER Operator Site 2 OR Site 3 to cause complete repression

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If operator sites 2 and 3 are missing from the lac operon, how does this affect repression?

Repression is reduced (not abolished)

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If operator site 1 is missing from the lac operon, how is repression affected?

Repression is nearly abolished

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The activator protein for the lac operon is the ______ protein

CAP

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The activator protein for the lac operon binds to the _____ site

CAP

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How does cAMP interact with the CAP Protein

cAMP functions as an effector molecule, meaning that when cAMP levels are high, cAMP binds to the CAP PROTEIN and the CAP protein is thus induced to bind to the CAP Site

What is attenuation (as seen with the trp operon)?

tRNAs play a role in which transcription stops before the entire mRNA sequence is made

What is a riboswitch?

An RNA molecule can exist in two different secondary conformation (one being active while the other inhibits gene expression) Conversion to one to the other is due to the binding of a small molecule

A riboswitch can regulate (transcription/translation)

Translation

In Eukaryotes, what is a transcription factor?

Protein that influences the ability of RNA polymerase to transcribe a given gene

How do transcription factors regulate transcription (2 ways)?

1) Regulate the binding of RNA polymerase to CORE PROMOTER 2) Control switch from initiation to elongation

Regulatory Transcription factors recognize \_\_\_\_\_\_- acting elements often located in the vicinity of the CORE PROMOTER

Cis

What are the two types of transcription factors in eukaryotes?

Activator and Repressor

An activator TF binds to a(n) (enhancer/repressor) sequence to (increase/decrease) transcription

Enhancer, Increase

A repressor TF binds to a(n) (enhancer/silencer) sequence to decrease transcription

In eukaryotes, what is combinational control?

Phenomenon in which eukaryotic genes are regulated by many factors (i.e. many activators and repressors acting in concert). The combination of these factors determines gene expression

Most regulatory transcription factors do not bind directly to RNA polymerase. Instead, they function via......

Mediators

What are the two types of mediators that Regulatory TFs use?

1) TFIID 2) Mediator (it's literally called mediator, Mediator and TFIID are both types of mediators. Dont get this confused)

What is TFIID and how does it function?

A transcription factor that binds to the TATA Box; it is needed to recruit RNA Polymerase II to the Core Promoter

What is Mediator and how does it function?

This is a protein complex which regulates the interaction between RNA Polymerase II and Regulatory TFs

How do transcriptional activators influence the ability of Mediator to switch from initiation to elongation?

They stimulate the switch from initiation to elongation

What is the Chromatin Remodeling Complex?

A protein complex that recognizes nucleosomes and uses ATP to alter nucleosome configuration

What are the three effects possible that the Chromatin Remodeling Complex can do?

1) Change the position of nucleosomes 2) Remove Histones to create gaps 3) Replace histones with histone variants

What are histone variants?

These are variants of histones which all have different functions regarding chromatin structure.

How does the histone code control gene transcription?

Specifies alterations in chromatin structure, such as acetylation or phosphorylation of specific histone units (this affects transcription)

Active genes (or genes that can be activated) have their core promoter at a ________ \_\_\_\_\_\_\_\_ \_\_\_\_\_\_\_ (Hint: The acronym is NFR)

Nucleosome Free Region

What is DNA methylation?

The covalent attachment of methyl groups to DNA structure

DNA Methylation occurs on what DNA base (A,G,T or C)?

Cytosine

DNA methylation (inhibits/activates) transcriptional initiation

INHIBITS

What are CpG islands?

Sequences of DNA that contain a high number of Cytosine bases which can be methylated

Where are CpG Islands usullay located along a DNA strand?

Near the promoters of genes

T/F Methylation of CpG islands only prevent the binding of RTFs to the promoter region

False, they can also enhance the binding of certain RTFs

Genomic Imprinting occurs during.....

Gamete Formation

Methylation can occur at what two sites?

1) Imprinting-Control Region (IRC) 2) Differentially Methylated Region (DRG)

Describe how the Igf2 gene copy from the mother is silenced. (Hint: This involves methylation)

In oogenesis, both the IRC and DGR are unmethylated. Instead CTC-binding factor binds to these regions. The CTCFs can then bind to each other to form a loop. The loop structure prevents an enhancer from stimulating the igf2 gene (which turns it off)

Describe how the paternal copy of igf2 is not silenced.

In spermatogenesis, the ICR and DGR are methylated. This methylation prevents CTCFs from binding, and no loop forms as a result. No loop means the enhancer can stimulate the Igf2 gene

What are ncRNAs?

These are non-coding RNAs, which are RNA molecules that do NOT encode a polypeptide

What types of molecules can ncRNAs bind to?

1) Proteins and small molecules 2) DNA and RNA

HOTAIR is an example of what type of RNA?

non-coding RNA

HOTAIR (activates/represses) gene transcription and alters chromatin structure

Represses

What types of ncRNA is HOTAIR? (Hint: It is 2 types)

Guide and Scaffold

How does HOTAIR function?

What is RNA interference (RNAi)?

A process in which a double stranded RNA causes the silencing of mRNA

Micro RNAs (miRNAs) are (exogenous/endogenous)

Endogenous (transcribed from eukaryotic genes)

How do miRNAs work?

They bind to a complementary mRNA

miRNAs influence (transcription/translation)

Translation

What is the overall affect of miRNAs on translation?

They inhibit Translation

T/F One miRNA can bind to multiple mRNA

True

T/F miRNAs are a perfect match to the complementary mRNA they bind to

False, they are a close match but not perfect

siRNAs orignate from (endogenous/exogenous) sources (Hint: siRNAs can be aquired via viral infection)

Exogenous

T/F siRNAs are a perfect match to one type of mRNA

True

RNAi is a mechanism of RNA silencing in which _______ or ________ becomes part of a RNA Induced Silencing Complex that (inhibits/promotes) translation of a specific mRNA or causes its degradation

1) miRNA, siRNA 2) Inhibits

The degradation of mRNA via RISC in RNAi usually occurs with (miRNAs/siRNAs)

siRNAs

The inhibition of translation via RISC without degrading mRNA occurs more frequently with (siRNAs/miRNAs)

miRNAs

Describe the relationship between ncRNAs and Protein Targeting

Protein targeting is assisted by an RNA complex called the Signal Recognition Particle (SRP) SRP labeling then allows the protein to be moved to a specific location

What is the Signal Recognition Particle (SRP)

An RNA complex used in Protein Targeting. It is composed of one ncRNA and one or more proteins.

The insertion of a transposable element (TE) into a gene tends to (activate/inactivate) that gene

Inactivate

What are piRNAs?

ncRNAs that associate with a class of proteins called PIWI proteins

How do piRNAs affect Transposable Elements?

They silence Transposable Elements

\_\_\_\_\_\_\_ Proteins prevent undesirable TE insertions from being passed from parent to offspring

PIWI

In what type of cells are PIWI proteins typically expressed? Hint: PIWI proteins prevent undesirable TE insertions from being passed down to offspring

In germ line cells

In gene cloning, what is a vector?

A small DNA molecule that replicates independently of the Chromosomal DNA. It produces many copies of an inserted gene.

Describe gene cloning using vectors

A gene is removed from its native site in the chromosome. It is inserted into a vector. The vector acts as a carrier oof the DNA segment to be cloned.

T/F Cloning DNA can be made from RNA via reverse transcriptase

True

Does Polymerace Chain Reaction (PCR) require vectors/host cells?

What 3 steps does each cycle of PCR involve?

1) Denaturation 2) Primer Annealing 3) Primer Extension

In PCR, the DNA of interest is located between two....

Primers

The end result of PCR is that the region flanked by the two primers is......

Amplified