Chapter 18- Lecture Outline

Question 1

Prokaryotes and eukaryotes precisely regulate gene expression in response to environmental conditions
In multicellular eukaryotes, gene expression regulates development and is responsible for differences in cell types

Answer 1

RNA molecules play many roles in regulating gene expression in eukaryotes

Question 2

Natural selection has favored bacteria that produce only the products needed by that cell

Answer 2

A cell can regulate the production of enzymes by feedback inhibition or by gene regulation
One mechanism for control of gene expression in bacteria is the operon model

Question 3

A cluster of functionally related genes can be coordinately controlled by a single “on-off switch”

Answer 3

The “switch” is a segment of DNA called an operator usually positioned within the promoter

Question 4

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

Answer 4

operon

Question 5

The operon can be switched off by a protein repressor

Answer 5

The repressor prevents gene transcription by binding to the operator and blocking RNA polymerase
The repressor is the product of a separate regulatory gene

Question 6

The repressor can be in an active or inactive form, depending on the presence of other molecules

Answer 6

A corepressor is a molecule that cooperates with a repressor protein to switch an operon off
For example, E. coli can synthesize the amino acid tryptophan when it has insufficient tryptophan

Question 7

By default the trp operon is on and the genes for tryptophan synthesis are transcribed

Answer 7

When tryptophan is present, it binds to the trp repressor protein, which turns the operon off
The repressor is active only in the presence of its corepressor tryptophan; thus the trp operon is turned off (repressed) if tryptophan levels are high

Question 8

A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription

Answer 8

The trp operon is a repressible operon
An inducible operon is one that is usually off;a molecule called an inducer inactivates the repressor and turns on transcription

Question 9

The lac operon is an inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose

Answer 9

By itself, the lac repressor is active and switches the lac operon off
A molecule called an inducer inactivates the repressor to turn the lac operon on

Question 10

Inducible enzymes usually function in catabolic pathways; their synthesis is induced by achemical signal

Answer 10

Repressible enzymes usually function in anabolic pathways; their synthesis is repressed by high levels of the end product
Regulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor

Question 11

Some operons are also subject to positive control through a stimulatory protein, such as catabolite activator protein (CAP), an activator of transcription

Answer 11

When glucose (a preferred food source of E. coli) is scarce, CAP is activated by binding with cyclic AMP (cAMP)
Activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription

Question 12

When glucose levels increase, CAP detaches from the lac operon, and transcription returns to a normal rate

Answer 12

CAP helps regulate other operons that encode enzymes used in catabolic pathways

Question 13

All organisms must regulate which genes are expressed at any given time

Answer 13

In multicellular organisms regulation of gene expression is essential for cell specialization

Question 14

Almost all the cells in an organism are genetically identical
Differences between cell types result from differential gene expression, the expression of different genes by cells with the same genome

Answer 14

Abnormalities in gene expression can lead to diseases including cancer
Gene expression is regulated at many stages

Question 15

The structural organization of chromatin helps regulate gene expression in several ways

Answer 15

Genes within highly packed heterochromatin are usually not expressed
Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression

Question 16

In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails

Answer 16

This loosens chromatin structure, thereby promoting the initiation of transcription
The addition of methyl groups (methylation) can condense chromatin; the addition of phosphate groups (phosphorylation) next to a methylated amino acid can loosen chromatin

Question 17

DNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species

Answer 17

DNA methylation can cause long-term inactivation of genes in cellular differentiation
In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development

Question 18

Although the chromatin modifications just discussed do not alter DNA sequence, theymay be passed to future generations of cells

Answer 18

The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance

Question 19

Chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either

Answer 19

more or less able to bind the transcription machinery

Question 20

Associated with most eukaryotic genes are multiple control elements, segments of noncoding DNA that serve as binding sites for transcription factors that help regulate transcription

Answer 20

Control elements and the transcription factors they bind are critical to the precise regulation of gene expression in different cell types

Question 21

To initiate transcription, eukaryotic RNA polymerase requires the assistance of transcription factors

Answer 21

General transcription factors are essential for the transcription of all protein-coding genes
In eukaryotes, high levels of transcription of particular genes depend on control elements interacting with specific transcription factors

Question 22

Proximal control elements are located close tothe promoter

Answer 22

Distal control elements, groupings of which are called enhancers, may be far away from a geneor even located in an intron

Question 23

An activator is a protein that binds to an enhancer and stimulates transcription of a gene

Answer 23

Activators have two domains, one that binds DNA and a second that activates transcription
Bound activators facilitate a sequence of protein-protein interactions that result in transcription of a given gene

Question 24

Some transcription factors function as repressors, inhibiting expression of a particular gene by a variety of methods

Answer 24

Some activators and repressors act indirectly by influencing chromatin structure to promote or silence transcription

Question 25

A particular combination of control elements

Answer 25

can activate transcription only when the appropriate activator proteins are present

Question 26

Co-expressed eukaryotic genes are not organized in operons (with a few minor exceptions)

Answer 26

These genes can be scattered over different chromosomes, but each has the same combination of control elements
Copies of the activators recognize specific control elements and promote simultaneous transcription of the genes

Question 27

Loops of chromatin extend from individual chromosome territories into specific sites in the nucleus

Answer 27

Loops from different chromosomes may congregate at particular sites, some of which are rich in transcription factors and RNA polymerases
These may be areas specialized for a common function

Question 28

Transcription alone does not account for gene expression

Answer 28

Regulatory mechanisms can operate at various stages after transcription
Such mechanisms allow a cell to fine-tune gene expression rapidly in response to environmental changes

Question 29

In alternative RNA splicing, different mRNA molecules are produced from the same primary transcript,

Answer 29

depending on which RNA segments are treated as exons and which as introns

Question 30

The initiation of translation of selected mRNAs can be blocked by regulatory proteins that bind to sequences or structures of the mRNA

Answer 30

Alternatively, translation of all mRNAs in a cell may be regulated simultaneously
For example, translation initiation factors are simultaneously activated in an egg following fertilization

Question 31

The life span of mRNA molecules in the cytoplasm is a key to determining protein synthesis
Eukaryotic mRNA is more long lived than prokaryotic mRNA

Answer 31

Nucleotide sequences that influence the lifespan of mRNA in eukaryotes reside in the untranslated region (UTR) at the 3′ end of the molecule

Question 32

After translation, various types of protein processing, including cleavage and the additionof chemical groups, are subject to control

Answer 32

The length of time each protein function is regulated by selective degradation
Cells mark proteins for degradation by attaching ubiquitin to them
This mark is recognized by proteasomes, which recognize and degrade the proteins

Question 33

Only a small fraction of DNA codes for proteins, and a very small fraction of the non-protein-coding DNA consists of genes for RNA such as rRNAand tRNA

Answer 33

A significant amount of the genome may be transcribed into noncoding RNAs (ncRNAs)
Noncoding RNAs regulate gene expression attwo points: mRNA translation and chromatin configuration

Question 34

MicroRNAs (miRNAs) are small single-stranded RNA molecules that can bind to mRNA

Answer 34

These can degrade mRNA or block its translation

It is estimated that expression of at least half of all human genes may be regulated by miRNAs

Question 35

Small interfering RNAs (siRNAs) are similar to miRNAs in size and function

Answer 35

The blocking of gene expression by siRNAs is called RNA interference (RNAi)
RNAi is used in the laboratory as a means of disabling genes to investigate their function

Question 36

Some ncRNAs act to bring about remodeling of chromatin structure

Answer 36

In some yeasts siRNAs re-form heterochromatin at centromeres after chromosome replication

Question 37

Small ncRNAs called piwi-associated RNAs (piRNAs) induce heterochromatin, blocking the expression of parasitic DNA elements in

Answer 37

the genome, known as transposons

RNA-based regulation of chromatin structure is likely to play an important role in gene regulation

Question 38

Small ncRNAs can regulate gene expressionat multiple steps

Answer 38

An increase in the number of miRNAs in a species may have allowed morphological complexity to increase over evolutionary time
siRNAs may have evolved first, followed by miRNAs and later piRNAs

Question 39

During embryonic development, a fertilized egg gives rise to many different cell types

Answer 39

Cell types are organized successively into tissues, organs, organ systems, and the whole organism
Gene expression orchestrates the developmental programs of animals

Question 40

The transformation from zygote to adult results from cell division,

Answer 40

cell differentiation, and morphogenesis

Question 41

Cell differentiation is the process by which cells become specialized in structure and function
The physical processes that give an organism its shape constitute morphogenesis

Answer 41

Differential gene expression results from genes being regulated differently in each cell type
Materials in the egg set up gene regulation that is carried out as cells divide

Question 42

An egg’s cytoplasm contains RNA, proteins, and other substances that are distributed unevenly in the unfertilized egg

Answer 42

Cytoplasmic determinants are maternal substances in the egg that influence early development
As the zygote divides by mitosis, cells contain different cytoplasmic determinants, which lead to different gene expression

Question 43

The other important source of developmental information is the environment around the cell, especially signals from nearby embryonic cells
In the process called induction, signal molecules from embryonic cells cause transcriptional changes in nearby target cells

Answer 43

Thus, interactions between cells induce differentiation of specialized cell typesThus, interactions between cells induce differentiation of specialized cell types

Question 44

Determination irreversibly commits a cell to its final fate

Answer 44

Determination precedes differentiation

Cell differentiation is marked by the production of tissue-specific proteins

Question 45

Myoblasts are cells determined to produce muscle cells and begin producing muscle-specific proteins

Answer 45

MyoD is a “master regulatory gene” encodes a transcription factor that commits the cell to becoming skeletal muscle
The MyoD protein can turn some kinds of differentiated cells—fat cells and liver cells—into muscle cells

Question 46

Pattern formation is the development of a spatial organization of tissues and organs

Answer 46

In animals, pattern formation begins with the establishment of the major axes
Positional information, the molecular cues that control pattern formation, tells a cell its location relative to the body axes and to neighboring cells

Question 47

Pattern formation has been extensively studied in the fruit fly Drosophila melanogaster

Answer 47

Combining anatomical, genetic, and biochemical approaches, researchers have discovered developmental principles common to many other species, including humans

Question 48

In Drosophila, cytoplasmic determinants in the unfertilized egg determine the axes before fertilization

Answer 48

After fertilization, the embryo develops into a segmented larva with three larval stages

Question 49

Edward B. Lewis, Christiane Nüsslein-Volhard, and Eric Wieschaus won a Nobel Prize in 1995 for decoding pattern formation in Drosophila

Answer 49

Lewis discovered the homeotic genes, which control pattern formation in late embryo, larva, and adult stages

Question 50

Nüsslein-Volhard and Wieschaus studied segment formation

They created mutants, conducted breeding experiments, and looked for corresponding genes

Answer 50

Many of the identified mutations were embryonic lethals, causing death during embryogenesis
They found 120 genes essential for normal segmentation

Question 51

Maternal effect genes encode cytoplasmic determinants that initially establish the axes

Answer 51

of the body of Drosophila
These maternal effect genes are also called egg-polarity genes because they control orientation of the egg and consequently the fly

Question 52

One maternal effect gene, the bicoid gene, affects the front half of the body

Answer 52

An embryo whose mother has no functional bicoid gene lacks the front half of its body and has duplicate posterior structures at both ends

Question 53

This phenotype suggests that the product of the mother’s bicoid gene is essential for setting up the anterior end of the embryo

Answer 53

This hypothesis is an example of the morphogen gradient hypothesis, in which gradients of substances called morphogens establish an embryo’s axes and other features of its form
Experiments showed that bicoid protein is distributed in an anterior to posterior gradient in the early embryo

Question 54

The bicoid research was ground breaking for three reasons
It identified a specific protein required for some early steps in pattern formation
It increased understanding of the mother’s role in embryo development

Answer 54

It demonstrated a key developmental concept that a gradient of molecules can determine polarity and position in the embryo