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225 Cards in this Set

  • Front
  • Back
______ must be able to quickly adapt to a changing environment
Prokaryotes
Gene control in Prokaryotes is all about
survival, conservation of ATP
Prokaryotes regulate genes in two ways; what are they?
1. Control the enzymes
2.Adjest the activity of enzymes already present
Bacteria try to control things pre_______
transcriptional
Bacteria only make ____ ATP per glucose
2
Bacteria use the _____ to regulate the production of enzymes
operon
The operon was discovered by
JAcob and Monod
When did Jacob and Monod discover the operon and when did they get the noble for it?
1961, 1965
JAcob served in the French_____
Army
Monod served in the french _____
resistance
Transcriptional unit is what?
DNA Strands that all have to be activated to make proteins
Genes for all enzymes needed to perform a single function are often linked together in _____ and not so much in _______
prokaryotes, eukaryotes
The switch upstream of the genes is called an
operator
An operator is positioned between the
promoter and structural genes
Structural genes are
enzyme coding genes
WHat is an operon?
promoter, operator, structural genes
An operon is, in essence, a
transcriptional unit
An operator is usually ___ by itself and can be turned _____ by a repressor protein binding to it
ON, OFF
REpressors are ____ for operators
specific
Gene that codes for this repressor protein is called a
regulatory gene
Repressor protein is ______
allosteric
Allosteric proteins have 2 forms. WHat are they?
Active and inactive form
trp REpressor protein is made in the ______ form with little affinity for the _____
inactive, operator
for trp Repressor, what turns it on?
present tryptophan
If the trp Repressor is on, what happens to the bacteria?
The gene expression is turned off.
With trp Repressor, what acts as a corepressor?
tryptophan
trp operon is said to be a
REpressible operon
What is a repressible operon?
OPeron that is repressed when a small molecule bnds to a regulatory protein
The terms active and inactive only work for
repressor molecule
small molecule is what?
Molecule that does feedback inhinition
A repressor is natively in the
inactive form
An anabolic pathway is
a building up process
Anabolism is when things are
built up
Anabolism takes ______ amounts of energy
large
Catabolism is
breaking things down
What is an operon?
Operator, transcriptional unit, promoter sequence
A metabolite is an
intermediate product between the precursor and final product
An inducible operon is stimulated when what?
A small molecule interacts with the repressor protein
In an inducible operon, what turns the operon on?
Small molecule combined with regulatory protein (red lego)
Inducible operons are
catabolic processes
Classic example of an inducible oepron is the
lac operon
what is an inducer and what does it do?
Small molecule that inactivates the repressor.
Repressible enzymes generally function in _____ pathways
anabolic
THe enzymes of the lactose pathway are reffered to as _____ enzymes because their synthesis is induced by a chemical signal
inducible
Regulation of both the trp and lac operons involves the ____ control of genes
negative
Explain how the lac operon is a negative control of genes
Allolactose induces enzyme synthesis not by acting directly on the genome but by freeing the lac operon from the negative effect of the repressor
When is gene regulation said to be positive?
WHen a regulatory protein interacts directly with the genome to switch transcription on.
If lactose is present in an inducible operon, what happens?
It binds to the repressor protein and the enzymes are made.
The inducer seduces he
lego away from the operator.
_____ are when the production of end product is stopped because it is already present
Repressible operon
______ are when enzymes aren't made when nothing is there
Inducible
NEgative gene regulation system is when the operons are swtitched off by the
ACTIVE form of the repressor molecule
The active form of the repressor molecule is when the
repressor protein sits on DNA
POsitive gene regulation is when some regulatory molecule
touches the DNA and turns the operon on
In a cell, if glucose levels are low, _____ levels are high
cAMP
cAMP is a _____ molecule
small
cAMP is what?
cyclic AMP
cyclic AMP has a _____ on 3' C
phosphate
cyclic AMP allows for
adrenaline
What are the monosaccharides?
Glucose, fructose, galactose
What are the disaccharides?
sucrose, maltose, lactose
cAMP binds to cAMP receptor protein, aka
CAP or CRP
when cAMP binds to CRP, it produces what?
An active form of CAP that binds to the CAP binding site just upstream of the promoter binding portion
CAP in the native form is
inactive
Attachment of active CAP to the CAP binding site does what?
Makes RNA polymerase bind tightly and make lots of lac enzymes quickly
CAP provides for ____ control
volume
if glucose is high, cAMP is
low
If there is glucose, what happens to the CAP?
Stays in the inactive form, doesn't bind with CAP binding site
The body prefers ______ not lactose
glucose
With glucose and lactose, what happens?
CAP is in active form. Body choose glucose but still eats lactose
Glucose and no lactose, what are conditions?
CAP is in inactive form, lac repressor bound, operon OFF
no glucose and no lactose, what are conditions?
CAP in active form, lac repressor on, operon OFF
ACtive CAP is like a
pinball machine
If someone is lactose intolerant, there are missing the gene that codes for
B- Galactosidase
The regulatory protein for cAMP is
CAP
CAP stands for
catabolite activator protein
The lac operon is under dual control:
negative by lac repressor and positive by CAP
No glucose and lactose, what are conditions?
Operon On, CAP active and bound, lac repressor off.
Eukaryotic organism regulates with more
complexity
Condensation is
wrapping up DNA
There are _____ histone proteins in a histone spool
8
At each end of the amino acid, there is an ___ terminus and an ______ terminus
N, C
The N terminus is the
amine end NH2
The C terminus is the
carboxyl end
The light bands on a chromosome are
euchromatin
Euchromatin are thought to be the
active parts of DNA
THe dark bands on a chromosome are thought to be ________ and represent the
heterochromatin, inactive parts of DNA
An Antibody is created by
B lymphocytes
THe ends of antibodies vary for what purpose?
They specifically attach to a foreign object via recognition glycoproteins
It is believed that your body can make antibodies for _______ disease or bacteria
any
The antibody has two _____ chains and two ____ chains
heavy, light
The variable regions in antibody DNA are called
V regions
What is the Somatic Recombination Hypothesis?
During cell differentiation DNA permanently changes into really rare form
WHat cells do somatic REcombination Hypothesis?
B and T lymphocytes
B & T lymphocytes starts as an undifferentiated cell that has the DNA for all possible
antigens
B & T lymphocyte cells cut out ________ in antibodies to make millions of different combinations
random variable genes
_______ is essential for cell specialization in multicellular organisms
REgulation of gene expression
A typical human cell might express about ____% of its protein coding genes at any given time
20
Almost all the cells in an organism contain an identical genome except cells of the
immune system
The differences between cell types are due to ________, or the expression of different genes by cells with the same genome
differential gene expression
When gene expression proceeds abnormally, ______ can arise
cancer or serious abnormalities
A common control point for gee expression for all organisms is at
transcription
Regulation at transcription is usually due to
outside signals
Gene expression is often equated with
transcription for both bacteria and eukaryotes.
_____ modification to histones play a direct role in the regulation of gene transcription
Chemical
The ___ terminus of each histone molecule in a nucleosome protrudes outward from the nucleosome
N
In _______, acetyl groups are attached to lysines at histone tails
Histone acetylation
______ is the removal of acetyl groups
Deacetylation
WHen lysines in Histones are acetylated, what happpens?
The charge is neutralzed and the histone tails no longer bind to neighboring nucleosomes
When the Histone spools unravel, what is likely to happen?
Transcription proteins have easier access to genes in an acetylated region.
Histone acetylation enzymes promote the intiaition of transcription by
1. remodeling chromatin structure
2.binding to and recruiting components of the transcription machinery
MEthyl and phosphate groups can be reversibly attached to ________ in histone tails
amino acids
Addition of a methyl group, or histone methylation, does what?
Promote condensation of the chromatin
Addition of a phosphate group (phosphorylation) to an amino acid next to a methyated AA can do what?
Promote uncondensation of chromatin
Histone code hypothesis says what?
Specific combinations of modifications, as well as order, help determine the chromatin configuration and transcription
When certain bases are methylated, what is the common one?
cytosine
what is DNA methylation?
WHen certain bases are mehthylated by enzymes
In what organisms does DNA methylation occur?
plants, animals, fungi
______ parts of DNA are generally more methylated than regions with _____ DNA
Inactive, active
Individual genes are more heavily methylated in cells in which they are
expressed
DNA methylation is essential for what in organisms?
Long term inactivation of genes
Deficient DNA methylation leads to _____ embryonic development
abnormal
What is genomic imprinting?
Methylation permanently regulates expression of either the maternal or paternal allele of particular genes at the start of development
Epigenetic inheritances are
Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence
What is a dual mechanism for repressing transcription?
MEthylating DNA while deacetylating histones
______ variations explain why one twin may get a genetic disease and the other does not
Epigenetic
________ enzymes provide intial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery
Chromatin modifying enzymes
What are control elements?
Segments of noncoding DNA that serve as binding sites for the proteins called transcription factors
______ in turn regulate transcription
Control Elements
General transcription factors are
transcription factors that are essential for the transcription of all protein-coding genes
Specific transcription factors are
control elements with another set of proteins
Chromatin modification means _______ is affected
DNA
Transcription modification means that _____ are affected
RNA
Transport to cytoplam modification means _______ is affected
RNA
translation modification means
protein is affected
All cells have copies of all genes except
B & T lymphocytes
WHat is a DNA binding domain?
How different proteins actually tough DNA
What are the three different types of DNA binding domains?
Helix Turn Helix
Zinc Fingers
Leucine Zippers
When there are arrows on a structure, it signifies a
B pleated sheet
When there are cylinders as a srtucture, it signifies
a helix
What is imprinting?
A phenomenon in which the phenotype matters on the source of the chromosome
Angelman and Prader-Willi are produced by a
deletion in chromosome 15
If there is a deletion in Dad's #15 chromosome, what disease occurs?
Prader-Willi
What are the symptoms of Prader-Willi?
Short, obese, moderate mental retardation, hungry, small hands and feet
A deletion in Mom's #15 chromosome produces what disease?
Angelman
What are the symptoms of Angelman disease?
Severe mental retardation, odd laughter outbursts, jerky uncontrolllable movements, large facial features, tongue thrusting and speech difficulties
Jerky Uncontrollable movements are produced by an
affected cerebellum
A normal person will express which #15 chromosome and and silent which #15 chromosome?
Mom is expressed, Dad off by imprinting
Mom's #15 chromosome is a gene for a type of
ubiquitin
What is ubiquitin used for?
Gettting rid of bad proteins
In Angelman's disease, what is the #15 chromosome that is expressed?
Neither
Usually, _____'s SNRPN by #15 gene is methylated into silence and ________'s works
Mom, Dad
If no SNRPN is produced by #15 gene, what is product?
PRader-Willi
What is the chromosome count of Turner's syndrome?
45, XO
Turner's syndrome is another form of
imprinting
What are the symptoms of Turner's syndrome?
Short of stature, neck webbing, no secondary sex characteristic, extremely nuturing, docile, infertile, shield chest
In Turner's syndrome, if X comes from MOm, what is the result?
Higher degree of survivability
In Turner's syndrome, if X comes from Dad, what is the result?
Higher people skills
Distal control elements are ___ from DNA
far
Proximal control elements are ______ to DNA
close
Positive gene regulation in prokaryotes can ________ the transcription of certain genes
fine tune
A negative gene control acts as an
on or off switch
Transcription initiation complex is what?
Collection of proteins that forms upstream of the gene
What are control elements?
Segments of noncoding DNA that serve as binding sites for transcription factors
What are general transcription factors?
Transcription factors that are essential fr the transcription of all protein coding genes
Specific transcription factors are
set of proteins that interact with control elements of particular genes at the appro time and place
Proximal control elemts are located
close to the promoter
Enhancers are what?
groupings of distal control elements
Activators and repressors are
specific transcription factors
Activators or repressors bind to
control elements of enhancers
What is the DNA binding domain?
protein's three dimensional structure that binds to DNA
Activation domains are
domains that bind to other regulatory protein or components of the transcription machinery, facilitating protein-protein interations
What are the two common elements that are part of activator proteins?
DNA binding domain, activation domains
Activators bind to _______ and then ________
enhancer DNA sequences, mediator proteins
After activator binds to two different protein structures, what does it bind into?
General transcription factors which then assemble the transcription initiation complex
Mediator protein complexes help
assemble and position of the initiation complex on the promoter
What are some ways repressors work?
binding to control element DNA, turning off transcription, blocking the binding of activators to proteins
Some activators and repressors work indirectly by affecting _____ structure
chromatin
Silencing is when
repressors recruit proteins that deacetylate histoness, leading to reduced transcription
There is not great ______ in control elements
variability
There are a ______ sequences used for control elements repeatedly
dozen
It is the _______ of control elements that is important in regulating transcription
combination
Coordinate gene expression depends on the association of specific combination of ______ with every gene
control elements
______ hormone enters a cell and binds to a specific intracellular receptor protein
steroid
_____ hormone can make a hormone receptor complex
steroid
Hormone receptor complex acts as a
transcription activator
________ hormones bind to receptors on a cell's surface but do not ever enter the cell
Nonsteroid
_____% of human genes have multiple exons that have undergone alternative splicing
75-100
UTR is the
untranslated region of mRNA (3' end)
Regulatory proteins are activated or inactivated by
the addition of phosphate groups
Proteasomes are
giant protein complexes
IN Eukaryotes, what is the first level of gene expression?
Chromatin
What are the three strategies of chromatin modification?
Histone acetylation, DNA methylation, Epigenetic inheritance
General and specific transcription factors are used to
increase mRNA production
Only ____% of DNA is protein coding
1.5
Some of the genome may be trancribed into _______ or ncRNAs
non protein coding RNA
microRNA's (miRNA) do what?
Capable of binding to complementary sequences in mRNA molecules
miRNA is made from
longer RNA precursors
The RNA precursor to miRNA fold back on themselves to make what structure held together by what force?
Hair pins structure held together by hydrogen bonds
After each "hairpin" of miRNA is cut away from the precursor, it is trimmed by what enzyme into what?
Dicer into a short double stranded fragment of 22 nucleotide pairs
The short fragment produced by the dicer is approx. _____ nucleotide pairs
22
One of the strands of miRNA is degraded while the other strand is
formed with a complex of proteins
The new miRNA complex allows whaT?
any miRNA molecule with 7-8 nucleotides of complementary sequence to bind
the miRNA protein complex has what function?
To either degrade the target mRNA or block its translation
RNAi is called
RNA intereferece
how does RNAi work?
RNA is injected to cell and stops gene expression
RNAi works because of
siRNA
What are siRNA?
small interfering RNA
The same cellular machinery that produces miRNA also produces
siRNA
siRNA are formed from
longer, linear, double stranded RNA molecule
piwi associated RNA (piRNA) are a class of
small ncRNA
piRNA can do what?
induce formation of heterochromatin, blocking expression of some DNA elements
Proteasomes know what proteins to eat because of the use of
ubiquitin
What RNA molecules are capable of binding to complementary sequences in mRNA molecules?
microRNA (miRNA)
at least what percent of human genes may be regulated by miRNA?
50%
____RNA and ____RNA are produced by the same cellular machinery
mi, si
piRNA induce formation of ______ and block expression of __________
heterochromatin, transposons
What are transposons?
parasitic DNA elements
piRNA are _______ nucleotides long
24-31
piRNA are probably processed from
RNA precursors
An example of specific transcription factor is an
activator
______ to ________ interactions facilitate the correct positioning of the promoter complex and the initiation of RNA synthesis
protein, protein
Transcription factories are what?
Different loops from the same chromosome and loops from other chromosomes may congregate in sites that are rich in RNA polymerases and other trasncription associated proteins
_____ are thought to be areas specialzed for a common function.
transcription factories