Module 3 - Gene Expression Regulation Flashcards
- 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
Gene expression is _________ to ensure that the correct proteins are made when and where they are needed.
regulated
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.
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
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
in eukaryotic organism, the type and amount of protein is regulated by ________
controlling gene expression
To express a protein, the _____ is first transcribed into _______, which is then translated into ________.
DNA
RNA
proteins
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
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
the mechanisms and systems that control the expression of genes
Gene Regulation
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)
Why regulate gene expression?
For the cell or organisms to: (3)
- adjust to sudden changes
- conserve energy
- save resources
all of the mechanisms involved in regulating gene expression
gene control
gene control (2)
which the most common gene control
- regulation of transcription (most common)
- mechanisms influencing the processing, stabilization, and translation of mRNAs
provided a molecular basis for the connection between genotype and phenotype
central dogma
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
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
encode proteins that are used in metabolism or biosynthesis or that play a structural role in
the cell
Structural Genes (ex: lac operon)
- 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)
the products of regulatory genes are
DNA-BINDING PROTEINS
a few genes (particularly those that encode essential cellular functions) that are expressed continually
Constitutive genes (ex: housekeeping gene)
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)
The regulation of gene expression can be: (2)
- Positive control
- Negative control
regulation of gene expression that includes mechanisms or processes that stimulate gene expression
Positive control
regulation of gene expression that includes processes that inhibit gene expression
Negative control
positive or negative control?
- Promoter-catabolite repression system
- Inducible lac system
- Repressible trp system
- 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
tags
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.
phosphate, methyl, or acetyl groups
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.
nucleosome
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.
transcription factors
Transcription factors must bind to the promoter region first and recruit RNA polymerase to the site for transcription to be established
can bind to the promoter or enhancer regions and block transcription.
transcription repressors
Post-transcriptional control can occur at any stage after transcription, including (3)
RNA splicing, nuclear shuttling, and RNA stability
RNA is transported to the cytoplasm through
the
nuclear pore complex.
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
RNA-binding proteins (RPBs) and microRNAs (miRNAs)
As the _________ changes, the amount of time that
it is available for translation also changes.
stability
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
phosphorylated, acetylated, methylated, or ubiquitinated
- Cancer-causing mutations most often occur in two types of regulatory genes, called
a) proto-oncogenes and b) tumorsuppressor genes
are genes that normally help cells divide.
Proto-oncogenes
are genes that normally slow down or stop cell division
Tumor suppressor genes
