Chapter 18: Gene Regulation Flashcards
Inducible operons
operons/sequences that have a default mode of OFF, which PREVENT transcription; can be turned on when inducers attach to repressor proteins, then repressors attach to operon, enabling it to START transcription
lac operon is inducible
Non-coding RNA
ncRNA
RNAs that functions as gene expression regulators rather than coding for proteins during mRNA translation (and chromatin configuration)
Point mutation
a mutation affecting only one or very few nucleotides in a gene sequence.
Second messenger molecules
Small non-proteins molecules that pass along signals they receive after binding to ligand first messengers
cAMP is a second messenger
Ubiquitin
Chemical marker used to (in cahoots with microRNA) tag a protein as marked for recycling
Part of gene expression regulation in the cytosol
MicroRNA
aka miRNA
part of EUKARYOTE, cytosol-level gene regulation
small, regulatory (non-coding), single stranded RNAs that impact how long a ribosome can live/function. approx. 22 base pairs long
- Degrades mRNA in a miRNA complex (via ubiquitin and proteasome)
- Traps mRNA in a miRNA complex so the mRNA can’t go to the ER for translation
Inducers
molecules that turn on inducible operons
they bind to inactive repressor proteins, causing them to change shape, and then bind to the operator, thus ENABLING the RNA polymerase to translate the subsequent enzyme genes
Specific transcription factors
floater proteins that help turn SPECIFIC genes “on” or “off” by binding to control elements/binding sites on DNA
may cooperate with other proteins/transcription initiation complexes in order to facilitate transcription
Tryptophan operon
involves 5 genes for making tryptophan IN PROKAYOTES; default is “on”
turning it off is a famous example of gene repression
Pattern formation
process by which the various differentiated cells know where to grow
lac operon
involved in gene sequencing that makes enzymes for synthesizing glucose from lactose
when it’s in its default OFF status, RNA polymerase cannot translate the lactose digesting??? enzyme genes
3 ways proto-oncogenes become oncogenes
- Movement of DNA within the genome (causing increase in transcription)
- Number of photo-oncogenes increases
- Point mutations or changes in control elements increase photo-oncogene gene expression
Oncogenes
Genes associated with cancer
Morphogenesis
why/how our differentiated cells wind up in the correct locations (why your head doesn’t grow on your knee)
controlled by:
- cytoplasmic determinants
- Inductive signals cytoplasm and the environment it’s in
Promoter (sequence)
the binding site for RNA polymerase, the enzyme that performs transcription.
Alternative RNA Splicing
flexibility in assigning intron or extron status to sequences of RNA
part of eukaryote gene expression regulation; occurs during (pre)RNA Processing
Enhancer
What you call a bunch of distal control elements when they’re in a group
Differential Gene Expression
When cells with the same genome express different genes; why/how we have different types of cells with different specialities even though all the cells are clones
enables specialization of cells (liver cell vs penis cell)
Feedback inhibition
1 of 2 types of gene expression regulation IN PROKARYOTES
Effects enzymes involved in processing of substrates (unlike in co-repression, which effects the operators of the operon sequence)
Control Elements
segments of non-coding DNA that serve as binding sites for floater proteins called transcription factors
2 types: proximal and distal
Protein repressor
cock blocker IN PROKAYOTES!
protein that stops part of a gene sequence from being expressed
req. co-repressors in order to work; lays inactive until the co-repressor binds to it, causing it to change shape, and then bind to the operator, thus preventing the RNA polymerase from transcribing the subsequent sequence
Induction
When signal molecules from embryonic cells cause transcription changes in nearby target cells (causing them to specialize); Involves:
- signaling molecule
- signal receptor
- signal transduction pathway
DNA methylation
2 of 2 types of EUKARYOTE, chromatin-level gene regulation
methyl groups (CH3-) are attached to certain bases (usually cytosine) to reduce its transcription
Repressible operons
have a default mode of ON, which ENABLES transcription. Can be switched off if a repressor is attached to its operator
tryp operon is repressible
Proximal Control element
DNA sequence; type of control element found close to the DNA strand promotor sequence it needs to use
used in transcription level gene regulation in eukaryotes
Operator
on/off switch of the PROKARYOTIC operon sequence
turns genes on and off
Regulatory gene
aka Regulator gene
a gene (DNA sequence) involved in controlling the expression of one or more other genes.
exp. regulator genes makes repressors
DNA bending protein
Can fold the DNA strand over on itself so that far away activators can reach their actions sites using a transcription initiation complex
Proto-oncogenes
Healthy genes that correspond with genes that cause cancer
Responsible for normal growth/division
Operon
IN PROKAYOTES!!! mostly
Series if sequences in a DNA strand that includes its promotor, operator, and structural genes that they control
(this whole group of sequences makes up the operon)
Proteasome
Enzymes that recognize and destroy/degrade proteins that have a ubiquitin marker
Part of gene expression regulation in the cytosol
Inductive signaling
environmental factors (especially r/t other, nearby cells) around a fertilized egg that effect its development/gene expression
Distal control element
part of DNA sequence; type of control element that may be found farther away/ way before or way after the promoter it needs to use, or located in different introns
usually only effects one gene
called ‘enhancers’ when they’re in a group
Positive gene regulation
DELETE THIS CARD?
involves inducement/acceleration
histone acetylation
1 of 2 types of EUKARYOTE, chromatin-level gene regulation
acetyl groups are attached to the positively charged lysine on histone tails, causing the chromatin to loosen
looser chromatin = better for transcription
Determination
the process by which cells are ‘instructed’ in what to specialize into (via expression master regulatory genes like MyoD in the precursor cells), whose expression is trigger by signals from nearby cells
Tryptophan Co-repressor fx when not in use
can be recycled for synthesizing tryptophan when it isn’t bound to the tryptophan repressor protein
Cytoplasmic determinants
factors in a fertilized egg’s cytoplasm the effect its development/gene expression.
Coded for by maternal effect genes
Myoblast
what you call a cell that is destined (by determination) to become a muscle cell.
Co-repression
1 of 2 types of gene expression regulation IN PROKARYOTES
Acts on the operons that regulate the genes that make materials that process substrates (unlike feedback inhibition, which effects the actual enzymes)
When the (sufficient or excessive) quantity of a particular substance triggers repression of the genes used to produce enzymes for breaking/building that substance
Negative Control
when gene expression is regulated by turning an operon OFF using the active (not dormant) form of the repressor in PROKARYOTES!
used in regulation of tryp and lac operons
Embryonic lethals
What Nusslein-Volhard and Wieschaus called it when mutations caused death before birth
cAMP
Cyclic adenosine monophosphate
Type of second messenger molecule that activates proteins
Made from ATP
Catabolite activator protein (CAP)
example of a an activator protein (for inducement)
is turned on by messenger protein cAMP (the two bind together, then change shape, then bind to the RNA promotor so the polymerase can transcribe)
3 fx of Tumor suppression genes
Help prevent uncontrolled growth (when they’re working right) by:
- preparing damaged DNA
- controlling cell adhesion
- inhibiting the cell cycle (via cell-signaling pathways)
Transcription initiation complex
complex made of:
activators
mediator proteins
general transcription
RNA pol II
that clump together (as DNA bending proteins fold the strand over itself) in order to bring the control element to the promotor for transcription
Maternal effect genes
aka egg polarity genes
genes that encode for the cytoplasmic determinants that effect the fertilized egg’s phenotype (exp. bicoid gene)
Mutations may be passed down by this pathway, regardless of the egg’s genotype
7 times EUKARYOTES can regulate gene expression
- during chromatin unpacking
- during transcription
- during RNA processing
- during transport to cytoplasm
- during translation
- during protein processing
- during transport to cellular destination
“Ras” proto-onco gene
may lead to overproduction of ras protein when mutation occurs
cells respond by producing more cells faster
Transcription factors
floater proteins that help turn genes “on” or “off” by binding to control elements/binding sites on DNA in order to help the RNA polymerase??? attach/transcribe
may cooperate with other proteins/transcription initiation complexes in order to facilitate transcription
2 types: general and specific
Homeotic genes
what Edward Lewis called it when mutant flies in his research presented with genetic abnormalities (like extra wings or legs in the wrong places)
Transcription factor domains (2)
- DNA binding domain (binds to DNA strand)
2. DNA activation domain (binds to other proteins/transcription complexes to facilitate transcription)
Morphogens
Factors in the embryonic environment that orient the axis of it’s development (so the head grows on top, and the feet grow at the bottom)
these exist on a gradient
Epigenetic inheritance
The inheritance of traits transmitted by mechanisms not directly involving nucleotide sequence
Involves expression modifications that do not alter the DNA sequence but can be passed to future generations of cells
Bicoid gene
Protein; Exp. of maternal effect gene; effects the front half of the body
Lack of this factor in the embryonic environment will result with offspring with two assholes and no head.
Positional information
the molecular cues that control pattern formation (so you don’t grow a foot on your face)
Edward Lewis studied this with mutant flies who had legs on their heads
General transcription factors
floater proteins that GENERALLY help turn genes “on” or “off” by binding to control elements/binding sites on DNA IN EUKARYOTES
may cooperate with other proteins/transcription initiation complexes in order to facilitate transcription???
required for the transcription of ALL eukaryotic genes.
may bind to the TATA box promoter site of the DNA