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