1
Q
coordinately controlled
A
genes of related function grouped into one transcription unit; a single “on-off switch” controls the whole cluster of functionally related genes.
2
Q
operator
A
- the “switch”
- positioned within the promoter OR btwn the promoter and the enzyme-coding genes
- controls the access of RNA polymerases to the genes
3
Q
operon
A
operator + promoter + the genes they control
4
Q
repressor
A
- protein that can switch off the operon
- binds to operator and blocks attachment of RNA pol to the promoter, preventing transcription of the genes
- specific for the operator of a particular operon
5
Q
regulatory gene
A
- located some distance from the operon and has its own promoter; its protein product is a repressor
- regulatory genes are expressed contiuously, although at a low rate
- the repressor is synthesized in an inactive form w/ little affinity for the operator; only if tryptophan binds to the repressor at an allosteric site does the repressor protein change to the active form that can attach to the operator, turning the operon off
6
Q
corepressor
A
- a small molecule that cooperates w/ a repressor protein to switch an operon off
- as tryptophan accumulates, more tryptophan molecules associate w/ trp repressor molecules, which can then find to the trp operator
7
Q
repressible vs inducible operon
A
- repressible: its transcription is usually on but can be repressed when a specific small molecule binds allosterically to a repressor; ex: trp operon. generally function in anabolic pathways.
- inducible operon: usually off but can be stimulated; ex: lac operon. enzyme synthesis is induced by a chemical signal. generally function in catabolic pathways.
8
Q
lactose metabolism
A
begins w/ hydrolysis of the disaccharide into its component monosaccharides, glucose and galactose, a rxn catalyzed by the enzyme beta-galactosidase
9
Q
trp operon
A
- 5 genes controlled by a single promoter
- by itself, the trp operon is turned on – trp is produced
- the regulatory gene trpR produces the trp protein repressor
- [ repressor + tryptophan (corepressor) ] binds to trp operator, shutting down trp production
10
Q
lac operon
A
- includes 2 other genes coding for enzymes that function in lactose utilization
- by itself, lac operon is turned on – beta-galactosidase is produced
- regulatory gene lacI(i), located outside the operon, codes for a repressor protein that is ACTIVE BY ITSELF. when this repressor binds to lac operon, beta-galactosidase is not produced
- when an INDUCER (allolactose, an isomer of lactose formed in small amounts from lactose that enters the cell) binds to the repressor, the repressor can’t bind to the operator, and beta-galactosidase is produced.
11
Q
inducer
A
specific small molecule that inactivates the repressor it binds to –> genes are expressed
12
Q
negative vs positive gene regulation
A
- negative: the operons are swithced off by the active form of the repressor protein
- positive: when a regulatory protein interacts directly w/ the genome to switch transcription on
13
Q
positive control of lac operon
A
- cAMP accumulates when glucose is scarce
- catabolite activator protein, CAP, is an ACTIVATOR, a protein that binds to DNA and stimulates transcription of a gene
- when cAMP binds to CAP, CAP assumes its active shape and can attach to a specific site at the upstream end of the lac promoter
- this attachment increases the affinity of RNA polymerase for the promoter, and beta-galactosidase is produced
- even when amount of glucose increases, transcription of the lac operon still proceeds at a low level; CAP controls RATE of transcription
14
Q
other uses of CAP
A
helps regulate other operons that code enzymes used in catabolic pathways; may affect the expression of >100 genes in E. coli
15
Q
histone modifications
A
- histone acetylation: acetyl groups (-COCH3) are attached to LYSINES in histone tails. when the lysines are acetylated, their positive charges are neutralized and the histone tails no longer bind to neighboring nucleosomes. when this binding doesn’t occur, chromatin has a looser structure, and as a result, transcription proteins have easier access to genes in an acetylated region. some acetylation enzymes are closely related to transcription factors.
- methylation: (-CH3) can promote condensation of the chromatin
- phosphorylation: addition of phosphate group to an AA next to a methylated AA can have the opposite effect
16
Q
DNA methylation
A
- enzymes methylate certain bases in DNA, usually CYTOSINE
- occurs in most plants, animals, fungi
- inactivates genes (ex: Barr bodies)
- cells forming speicalized tissues keep a chemical record of what occurred during embryonic development – methylation patterns are passed down. a methylation pattern maintained in this way also accounts for genomic imprinting in mammals, where methylation permanently regulates expression of either the maternal or paternal allele of particular genes at the start of development
17
Q
epigenetic inheritance
A
- Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence of a genome.
- involves modification of chromatin structure.
18
Q
control elements
A
- associated w/ most eukaryotic genes
- segments of noncoding DNA that serve as binding sites for transcription factors
- proximal and distal
19
Q
enhancers
A
- groupings of distal control elements (10 on avg); each control element can bind 1 or 2 activators/repressors
- may be thousands of nucleotides upstream / downstream of a gene or even within an intron
- a given gene may have multiple enhancers, each active at a diff time or in a diff cell type or location; each enhancer is associated w/ only that gene
20
Q
high vs low levels of transcription
A
- high: depend on the interaction of control elements w/ SPECIFIC TRANSCRIPTION FACTORS (activators/repressors)
- low: interaction of general transcription factors and RNA pol II w/ a promoter
21
Q
enhancers and specific transcription factors: process
A
- activators bind to enhancer (groups of distal control elements).
- a DNA-bending protein brings the bound activators closer to the promoter.
- the bound activators bind to certain mediator proteins and general transcription factors. these protein-protein interactions help them form an active transcription initiation complex on the promoter.
22
Q
indirect effects of specific transcription factors
A
- affect chromatin structure
- studies using yeast and mammalian cells show that some ACTIVATORS recruit proteins that acetylate histones near the promoters of specific genes, thus promoting transcription
- some REPRESSORS recruit proteins that deacetylate histones, leading to reduced transcription (SILENCING)
23
Q
liver vs lens cell
A
- only liver cells make ALBUMIN, a blood protein, and only lens cells make CRYSTALLIN, the main protein of the lens of the eye
- although the enhances for the two genes share one control element, each enhancer has a unique combo of elements
- it’s the COMBINATION of control elements, rather than the presence of a single unique control element, that is important in regulating transcription
24
Q
coordinately controlled genes in eukaryotes
A
- ex: genes coding for the enzymes of a metabolic pathway
- typically scattered over diff chromosomes
- coordinate gene expression depends on the association of a specific combination of control elements w/ every gene of a dispersed group
- copies of the activators that recognize the control elements bind to them, promoting simultaneous transcription of the genes, no matter where they are in the genome
- often occurs in response to chemical signals from outside the cell; ex: steroid hormone enters a cell and binds to a specific intracellular receptor protein, forming a hormone-receptor complex that serves as a transcription activator. every gene whose transcription is stimulated by a particular steroid hormone, regardless of its chromosomal location, has a control element recognized by the that hormone-receptor complex
25
chromosomal interactions
- in the interphase nucleus
- loops of chromatin extend from individual chromosomal territories into speicfic sites in the nucleus
- diff loops from the same chromosome and loops from other chromosomes may congregate in such sites, some of which are rich in RNA polymerases and other transcritpion-associated proteins
- "transcription factories"
26
example of a gene that undergoes alternative RNA splicing
troponin T gene. encodes 2 diff (though related) muscle proteins
27
mRNA degradation: bacteria vs multicellular eukaryotes
- nucleotide sequences that affect how long an mRNA remains intact are often found in the UTR at the 3' end of the molecule
- bacteria: mRNA typically degraded by enzymes within a few minutes of their synthesis
- eukaryotes: mRNA typically survive for hours, days, or even weeks
28
blocking translation
regulatory proteins bind to specific sequences/structures within the UTR at the 5' or 3' end, thus preventing the attachment of ribosomes
29
blocking translation in eggs
initially, stored mRNAs in eggs lack poly-A tails of sufficient length to allow translation initiation. at the appropriate time during embryonic development, a cytoplasmic enzyme adds more adenine nucleotides, prompting translation to begin.
30
post-translation processing
- regulatory proteins are commonly activated or inactivated by the reversible addition of phosphate groups, and proteins destined for the surface of animal cells acquire sugars.
- cell-surface proteins and many others must also be transported to target destinations in the cell in order to function.
31
protein degradation
1. to mark a particular protein for destruction, the cell commonly attaches molecules of a small protein called UBIQUITIN to the protein. (ATP required)
2. the tagged protein is recognized by a giant protein complex called a PROTEASOME, which unfolds the protein and sequesters it within a central cavity.
3. enzymatic components of the proteasome cut the protein into small peptides, which can be further degraded by other cytosolic enzymes. (ATP required)
32
ncRNAs
a significant amount of the genome may be trasncrbied into non-protein-coding RNAs, including a variety of small RNAs
33
miRNA
- microRNAs, small single-stranded RNA molcules that are capable of binding to complementary sequences in mRNA molecules
- miRNAs are made from longer RNA precursors that fold back on themselves, forming 1 or more short double-stranded hairpin structures, each held together by H bonds
34
miRNA function: the process
1. enzyme cuts each hairpin from the primary miRNA transcript.
2. a 2nd enzyme, Dicer, trims the loop and the single-stranded ends (at the opposite end of the loop) away from the hairpin.
3. one strand of the double strand is degraded; the other strand (the miRNA) forms a complex w/ 1 or more proteins
4. the miRNA in the complex can bind to any target mRNA that contains 7 to 8 nucleotides of complementary sequence.
5. the complex then either degrades the target mRNA or blocks its translation
35
RNAi
RNA interference; researchers found that injecting double-stranded RNA molecules into a cell somehow turned off expression of a gene w/ the same sequence as the RNA.
36
miRNA vs siRNA
- siRNA: small interfering RNA
- they're similar in size and function, generated by the same cellular machinery, and can associate w/ the same proteins
- miRNA is formed from a single hairpin in a precursor RNA
- multiple siRNAs are formed from a much longer, linear, double-stranded RNA molecule
37
evolutionary significance of RNAi
some viruses have double-stranded RNA genomes. b/c the cellular RNAi pathway can lead to the destruction of RNAs w/ sequences complementary to those found in double-stranded RNAs, this pathway may have evolved as a natural defense against infection by such viruses.
38
ncRNAs and chromatin
- small RNAs can cause remodeling of chromatin structure
- an RNA transcript produced from DNA in the centromeric region of the chromosome is copied into double-stranded RNA by a yeast enzyme and then processed into siRNAs. these siRNAs associate w/ a complex of proteins and target this complex back to RNA transcripts being made from the centromeric DNA sequences. once there, proteins in the complex recruit enzymes that modify the chromatin, turning it into the highly condensed heterochromatin found at the centromere.
39
piRNA
- class of ncRNAs; piwi-associated RNAs
- induce formation of heterochromatin, blocking expression of some parasitic DNA elements in the genome known as transposons.
- usually 24 to 31 nucleotides in length
- play impt role in germ cells of animals, where they help re-estalbish appropriate methylation patterns in the genome during gamete formation
40
evolutionary significance of ncRNAs
- siRNAs evolved first, then miRNAs, then piRNAs (piRNA only found in animals, thousands of types, allows for very sophisticated gene regulation)
- neRNAs play impt roles in embryonic development
41
cytoplasmic determinants
- the egg's cytoplasm contains both RNA and proteins encoded by mother's DNA
- mRNA, organelles, proteins are distributed unevenly in the unfertilized egg
- after fertilization, early mitotic divisions distribute the zygote's cytoplasm into separate cells
42
induction
- the environment around a particular cell is a major source of developmental info
- most influentail are the signals impinging on an embryonic cell from other embryonic cells in the vicinity, including contact w/ cell-surface molecules on neighboring cells and the binding of growth factors secreted by neighboring cells; such signals cause changes in the target cells
- the molecules conveying these signals send a cell down a specific developmental path by causing changes in its gene expression
43
structure of specific transcription factor
ex: the MyoD activator protein has 2 subunits w/ extensive regions of alpha helix. each subunit has a DNA-binding domain and an activation domain.
- myoD is the master regulatory gene for muscle cell differentiation.
44
determination and differentiation of muscle cells
1. determination: signals from other cells lead to activation of a master regulatory gene called myoD, and the cell makes MyoD protein, an activator. the cell, now called a myoblast, is irreversibly committed to becoming a skeletal mucle cell.
2. differentiation: MyoD protein stimulates the myoD gene further and activates genes encoding other muscle-specific transcription factors, which in turn activate genes for muscle proteins (ex myosin). MyoD also turns on genes that block the cell cycle, thus stopping cell division; the nondividng myoblasts fuse to become mature multinucleate muscle cells, also called muscle fibers.
45
pattern formation
The development of a multicellular organism's spatial organization, the arrangement of organs and tissues in their characteristic places in three-dimensional space. begins in the early embryo, when the major axes of an animal are established.
46
positional information
Molecular cues, provided by cytoplasmic determinants and inductive signals, that control pattern formation in an animal or plant embryonic structure by indicating a cell's location relative to the organism's body axes. These cues elicit a response by genes that regulate development.
47
homeotic genes
Any of the master regulatory genes that control placement and spatial organization of body parts in animals, plants, and fungi by controlling the developmental fate of groups of cells.
48
embryonic lethal
A mutation with a phenotype leading to death of an embryo or larva.
49
maternal effect gene
- a gene that, when mutant in the mom, results in a mutant phenotype in the offspring regardless of the offspring's own genotype
- in fruit fly development, the mRNA/protein products of these genes are placed in the egg while it's still in the mom's ovary; these eggs make defective gene products or none at all, and they fail to develop properly after fertilization
- also called egg-polarity genes b/c they control the oreitnation (polarity) of the egg (and consequently the fly); one group of these genes sets up the anterior-posterior axis of the embryo, while a second group establishes the dorsal ventral axis
- generally embryonic lethals
50
morphogen
- A substance, such as Bicoid protein in Drosophila, that provides positional information in the form of a concentration gradient along an embryonic axis. (morphogen gradient hypothesis)
- bicoid: 'two-tailed'; embryo whose mom has 2 mutant alleles of the bicoid genes has posterior structures at both ends
51
genetic changes that can turn proto-oncogenes into oncogenes
1. translocation/transposition: gene moved to new locus, under new controls (a more active promoter) --> growth-stimulating protein in excess
2. gene amplificiation: multiple copies of the gene --> growth-stimulating protein in excess
3. point mutation within a control element --> growth-stimulating protein in excess
4. point mutation within the gene --> hyperactive or degradation-resistant protein
52
oncogenes
cancer-causing genes in certain types of viruses. subsequently, close counterparts of viral oncogenes were found in the genomes of humans and other animals.
53
proto-oncogenes
normal versions of oncogenes. code for proteins that stimulate normal cell growth and division.
54
tumor-suppressor gene
- genes whose normal products inhibit cell division; their protein products help prevent uncontrolled cell growth
- any mutation that decreases the normal activity of a tumor-suppressor protein may contribute to the onset of cancer
- repair damaged DNA, control cell anchorage
55
ras gene
- named for rat sarcoma, a connective tissue cancer
1. growth factor binds to its receptor in plasma membrane
2. signal is relayed to a G protein called Ras. like all G proteins, Ras, is active when GTP is bound to it.
3. Ras passes the signal to a series of protein kinases.
4. the last kinase activates a transcription activator that turns on one or more genes for proteins that stimulate the cell cycle.
- mutations: may lead to production of a hyperactive Ras protein that triggers the kinase cascade even in the absence of growth factor --> excessive cell division
56
p53 gene
- named for the 53,000-dalton molecular weight of its protein product
1. DNA damage is an intracellular signal that is passed via protein kinases and leads to activation of p53
2. activated p53 promotes transcription of the gene for a protein that inhibits the cell cycle. the resulting suppression ensures that the damaged DNA isn't replicated. if DNA damage is irreparable, the p53 signal leads to apoptosis.
- mutations causing deficiencies in any pathway component can contribute to excessive cell division
57
many functions of p53 gene
- once it's activated, it functions as an activator for several other genes. often it activates the p21 gene, whose product halts the cell cycle by binding to cyclin-dependent kinases, allowing time for the cell to repair the DNA
- activates expression of a group of miRNAs, which in turn inhibit the cell cycle
- can turn on genes directly involved in DNA repair
- activates "suicide" genes for apoptosis
58
normal --> cancerous cell
- about half a dozen changes must occur at the DNA level
- these changes usually include the appearance of at least one active oncogene and the mutation/loss of several tumor-suppressor genes
- oncogenes behave as dominant alleles
- mutant tumor-suppressor alleles are usually recessive, so mutations must knock out both alleles to block tumor suppression
59
colorectal cancer development
1. loss of tumor-suppressor gene APC (or other) --> a polyp, a small benign growth
2. activation of ras oncogene + loss of tumor-suppressor gene DDC --> larger benign growth (adenoma)
3. loss of p53 + additional mutations --> malignant tumor (carcinoma)
60
APC
- tumor-suppressor gene called adenomatous polyposis coli
- regulates cell migration and adhesion
- mutated in 60 percent of colorectal cancers
61
breast cancer
- mutations in one gene, BRCA1, were associated w/ increased susceptibility to breast cancer
- w/ mutant BRCA1 allele: 60 percent chance of getting cancer before 500; w/o allele: 2 percent
- BRCA1 and BRCA2 are tumor-suppressor genes b/c their wild-type alleles protect against breast cancer; they both function in the cell's DNA damage repair pathway
