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Fall 2023 > BIOL. 1406 Chapter 18 Regulation of Gene Expression > Flashcards

BIOL. 1406 Chapter 18 Regulation of Gene Expression Flashcards

1
Q

How can two cells with the same set of genes function differently?

A

To be expressed, each gene requires a particular set of transcription factors.

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2
Q

Differential Gene Expression

A

The expression of different genes, allowing cells to carry their specific function.

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3
Q

Regulation of enzyme production by a cell

A

feedback inhibition and gene regulation

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4
Q

Feedback Inhibition

A

The end product of metabolic pathway shuts down further synthesis of the product by inhibiting enzyme activity.

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5
Q

Regulating Gene Expression

A

Adjusting production level of certain enzymes by a cell;
the control of enzyme production is thus at the level of transcription

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6
Q

Operon

A

the entire stretch of DNA that includes the operator, the promoter, and the genes that they control

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7
Q

Operator

A

A segment of DNA that acts as an on-off switch that can coordinate a cluster of functionally related genes

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8
Q

Repressor

A

A protein that switches off the operon;
it prevents gene transcription by binding to the operator and blocking RNA polymerase;
can be in an active or inactive form, depending on the presence of other molecules.

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9
Q

Regulatory Gene

A

A gene that is located some distance from the operon itself and produces the repressor protein

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10
Q

Corepressor

A

A molecule that cooperates with a repressor protein to switch an operon off.

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11
Q

Activator

A

A stimulatory protein that are used in positive control

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12
Q

Eukaryotic Gene Expression Is Regulated At Many Stages

A

all organisms must regulate which genes are expressed at any given time;
genes are turned off and on in response to the internal and external environments;
in multicellular organisms, regulation of gene expression is essential for cell specialization

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13
Q

Differential Gene Expression

A

Expression of different genes by cells with the same genome;
most of the time is equated with gene transcription

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14
Q

Chromatin

A

makeup of chromosomes in organisms other than bacteria; it includes DNA, RNA, and protein.

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15
Q

Expression Regulation by Chromatin Structure

A

The structural organization of chromatin helps regulate gene expression in several ways;
genes within highly packed heterochromatin are usually not expressed;
in euchromatin, gene transcription is affected by the location of nucleosomes;
chromatin structure and gene expression can be influenced by chemical modifications of the histone proteins on the nucleosome

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16
Q

Euchromatin

A

A lightly packed form of chromatin that is enriched in genes, and is often under active transcription

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17
Q

Nucleosome

A

a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones

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18
Q

Histone Acetylation

A

Acetyl groups are attached to an amino acid in a histone tail.
This appears to open up chromatin structure, thus promoting the initiation of transcription.

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19
Q

DNA Methylation

A

Addition of methyl groups to certain DNA bases;
associated with reduced transcription;
can cause long-term inactivation of genes in cellular differentiation;
Can change the activity of a DNA segment without changing the sequence

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20
Q

Epigenetic Inheritance

A

inheritance of traits transmitted by mechanisms not directly involving the nucleoside sequence

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21
Q

Control Elements

A

Segments of noncoding DNA that serve as binding sites for transcription factors that help regulate transcription

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22
Q

Specific Transcription Factors

A

A different set of factors that high levels of transcription depend on for genes that are not expressed all the time

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23
Q

Proximal Control Elements

A

Control elements that are located close to the promoter

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24
Q

Enhancers

A

distal control elements, groupings that may be far away from the gene or even located in an intron;
each enhancer is associated with only one gene and no other

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25
Q

Activator

A

a protein that binds to an enhancer and stimulates the transcription of a gene;
has two domains: one binds to DNA and the other one that activates the transcription;
bound activators facilitate a sequence of protein-protein interactions that result in enhanced transcription of a given gene

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26
Q

Mediator proteins

A

A group of proteins that that interact with general transcription factors at the promoter;
they come into contact with bound activators;
this helps assembly and position the preinitiation complex.

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27
Q

Transcription Factors in Gene Expression

A

Some act as repressors, inhibiting expression of a particular gene in several ways;
some repressors bind directly to control elements and block activator binding;
others interfere with activators, so they cannot bind the DNA;
some activators and repressors may indirectly affect transcription by altering chromatin structure.

28
Q

Combinatorial Control of Gene Activation

A

A particular combination of control elements can activate transcription only when the appropriate activator proteins are present;
with only a dozen or so control elements, a large number of potential combinations is possible

29
Q

Coordinately Controlled Genes in Eukaryotes

A

Co-expressed eukaryotic genes are not organized in operons (with a few exceptions);
these genes can be scattered over different chromosomes, but each has the same combination of control elements;
activator proteins in the nucleus recognize specific control elements and promote simultaneous transcription of genes

30
Q

Mechanisms of Post-Transcriptional Regulation

A

Transcription alone does not constitute gene expression;
regulatory mechanisms can operate at various stages after transcription;
such mechanisms allow a cell to rapidly fine-tune gene expression in response to environmental changes

31
Q

Alternative Splicing

A

different RNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which introns;
it significantly expands the repertoire of a eukaryotic genome;
proposed explanation for the surprisingly low number of genes in the human genome;
more than 90% of the human protein-coding genes undergo alternative splicing

32
Q

Initiation of translation

A

can be blocked by regulatory proteins that bind to sequences or structures of the mRNA;
may be regulated simultaneously

33
Q

Protein Processing and Degradation

A

after translation, polypeptides undergo processing and chemical modifications;
the length time each protein functions is regulated by selective degradation;
cells mark proteins for degradation by attaching ubiquitin to them;
the mark is recognized by proteasomes, which recognize and degrade proteins

34
Q

MicroRNAs (miRNAs)

A

small, single-stranded RNA molecules that can bind complementary sequences in mRNA;
these molecules along with associated proteins cause degradation of the target mRNA or sometimes block its translation;
at least one half of genes may be regulated by miRNAs

35
Q

Small Interfering RNAs (siRNAs)

A

similar to miRNAs in size and function;
used in laboratory as means of disabling genes to investigate their function;
used by bacteria as a defensive system, called CRISPR-Cas9 system, against viruses that infect them

36
Q

RNA Interference

A

blocking of gene expression by siRNAs

37
Q

Chromatin Remodeling and Effects on Transcription by ncRNAs

A

some ncRNA can cause remodeling of chromatin structure;
in some yeasts, siRNAs reform heterochromatin at centromeres after chromosome replication;
in most mammalian cells, siRNAs have not been found

38
Q

piwi-interacting RNAs (pRNAs)

A

small ncRNAs induce formation of heterochromatin, blocking the expression of parasitic DNA elements in the genome known as transposons;
help reestablish appropriate methylation patterns during gamete formation in many animal species

39
Q

Long noncoding RNAs (lncRNAs)

A

range from 200 to hundreds of thousands nucleotides in length;
one type is responsible for inactivation of the X chromosome;
can act as a scaffold, bringing DNA, proteins, and other RNAs together into complexes, promoting gene expression

40
Q

A program of differential gene expression

A

orchestrates the developmental programs of animals;
during embryonic development, a fertilized egg gives rise to many different types of cell;
cells are organized successfully into tissues, organs, organ systems, and organisms

41
Q

Genetic Program for Embryonic Development

A

transformation from zygote to an adult results from cell division, cell differentiation, and morphogenesis

42
Q

Cell differentiation

A

the process by which cells become specialized in structure and function;
a cell attains its determined fate

43
Q

Morphogenesis

A

the physical processes that give an organism its shape

44
Q

Cytoplasmic Determinants

A

maternal substances in the egg that influence early development;
as cells divides by mitosis, cells contain different cytoplasmic determinants, which lead to different gene expression

45
Q

Induction

A

a process, in which signal molecules from embryonic cells cause changes in the nearby target cells

46
Q

Determination

A

irreversibly commits a cells to become of particular type

47
Q

MyoD

A

a master regulatory gene that encodes a transcription factor that commits the cell to becoming skeletal muscle;
some encode information for production of additional muscle-specific transcription factors

48
Q

Pattern Formation

A

development of spatial organization of tissues and organs;
begins with the establishment of major axes

49
Q

Positional Information

A

molecular cues that control pattern formation, tells a cell its location relative to the body axes and neighboring cells

50
Q

Homeotic genes

A

genes that control pattern formation in the late embryo, larva, and adult stages in drosophila melanogaster

51
Q

Embryonic Lethals

A

mutations that cause death during embryogenesis

52
Q

Maternal Effect Genes

A

encode cytoplasmic determinants that initially establish the axes of the body of the drosophila

53
Q

Bicoid

A

one maternal effect gene that affects the front half of the body

54
Q

Morphogens

A

gradients of substances that establish an embryo’s axes and other features of its form

55
Q

Oncogenes

A

Genes, resulted from mutations in proto-oncogenes;
(proto-oncogenes code for proteins in regular cell growth and division);
arises from a change that leads to an increase either in the amount of protein product or in the activity of protein molecule

56
Q

genetic changes that convert proto-oncogenes into oncogenes

A

1) epigenetic changes 2) translocation 3) gene amplification 4) point mutations

57
Q

Tumor-suppressor genes

A

normally inhibit cell division;
mutations to these genes decrease protein products and contribute to cancer onset;
normally repair damaged DNA, control cell adhesion, and act in cell-signaling pathways that inhibit the cell cycle

58
Q

Interference with Normal Cell-Signaling Pathways

A

Mutations in the ras proto-oncogene and p53 tumor-suppressor gene are common in human cancers

59
Q

Ras gene

A

mutations in it can produce hyperactive ras protein and increased cell division

60
Q

Ras protein

A

a G protein that relays a signal from a growth factor receptor on the cell surface

61
Q

p53 gene

A

mutations in it prevent suppression of the cell cycle;
suppression of the cell cycle can be important in the case of damage to a cell’s DNA;
its normal version prevents a cell from passing on mutations;
it activates expression of miRNAs that inhibit the cell cycle, and can turn on genes directly involved in DNA repair;
it activates cell “suicide” genes;
elephants have 20 copies of p53 gene compared to just 1 copy in humans and other mammals (elephants have very low cancer rates 3%)

62
Q

The Multi-Step of Cancer Development

A

multiple mutation are generally needed for full-fledge cancer; incidents increase with age;
a DNA level, a cancerous cell is usually characterized by at least one oncogene and the mutation of several tumor-suppressor genes

63
Q

Inherited Predisposition and Environmental Factors Contributing to Cancer

A

Individuals can inherit oncogenes or mutant alleles of tumor-suppressor genes

64
Q

Adenomatous Polyposis Coli

A

tumor suppressor gene;
inherited mutations of it are common in individuals with colorectal cancer

65
Q

Mutations in the BRCA1 and BRCA2 genes

A

mutations found in at least half of inherited breast cancers, and tests using DNA sequencing can detect these mutations

66
Q

The role of viruses in cancer

A

a number of tumor viruses can also cause cancer in humans and animals;
viruses can interfere with normal gene regulation in several ways if they integrate into the DNA of a cell;
viruses are powerful biological agents

67
Q

General Transcription Factors

A

Factors that are essential for transcription of all protein-coding genes;
Their assistance is required by RNA Polymerase II to initiate transcription

Fall 2023 (14 decks)

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