Important words and concepts from Chapter 19,
Campbell & Reece, 2002 (1/29/2005):
by Stephen T. Abedon (abedon.1@osu.edu)
for Biology 113 at the Ohio State University
|
|
|
Course-external links are
in brackets Click [index] to access site index Click here to
access text’s website Vocabulary
words
are found below |
|
|
(1) Chapter title: Genome Organization and
Expression in Eukaryotes
(a)
[genome organization and
expression in eukaryotes (Google Search)] [index]
(a)
DNA in eucaryotic cells is organized into hierarchical structures
(b)
The less-condensed structures we've been calling chromatin
(c)
The most condensed structures we've been calling a chromosome
(d)
Note that gene transcription tends to decline as
organization/condensation increases; the more organized the DNA (regionally),
the less it is expressed
(e)
[structure of DNA (Google Search)] [index]
(a)
During interphase, DNA that is available for transcription is organized as chromatin
(b)
Chromatin consists of DNA wound around proteins
specialized for the task called histones
(c)
Higher levels of organization share the descriptive term, chromatin
(d)
See Figure 19.1a, Levels of
chromatin packing
(e)
[chromatin (Google Search)] [index]
(4)
Histones (nucleosome)
(a)
Histones are highly evolutionarily conserved proteins
(b)
They contain a high proportion of positively charged (basic) amino acids (lysine and arginine)
(c)
These positive charges interact with the negative charge of the
sugar-phosphate backbone of DNA
(d)
Individual histone-DNA complexes are called nucleosomes
(e)
[histone or histones,
nucleosome (Google Search)] [index]
(a)
Interphase DNA that is arrayed as chromatin
or slightly higher levels of organization (e.g., 30-nm fiber) is called
euchromatin
(b)
See Figure 19.1a &
19.1b, Levels of chromatin packing
(c)
Euchromatin is potentially available for transcription
(d)
[euchromatin (Google Search)] [index]
(a)
More tightly packed (condensed) interphase DNA is
called heterochromatin
(b)
See Figure 19.1.c and 19.1d,
Levels of chromatin packing
(c)
Heterochromatin is less available for transcription compared with euchromatin
(d)
Barr bodies, i.e., inactive X chromosomes,
consist mostly of heterochromatin
(e)
[heterochromatin (Google Search)] [index]
(a)
The ultimate level of chromosome condensation is achieved during prophase/prometaphase
(b)
See Figure 19.1d, Levels of
chromatin packing
(c)
The DNA within chromosomes is generally unavailable
for transcription
(d)
[chromosomes (Google Search)] [index]
(a)
The idea that organisms may adapt physiologically is one aspect of
phenotypic plasticity
(b)
In general, organisms are able to modify their phenotype in response to external cues by varying what genes
they express
(c)
We have already considered the control of gene expression in prokaryotes
(d)
Here we consider the control of gene expression
in the generally more-complex eukaryotes
(e)
[plasticity of phenotypes,
phenotype plasticity
(Google Search)] [index]
(9) Control of gene expression in eukaryotes, overview
(a)
Different cells, different
genes expressed
(i)
The various cell types of a multicellular organisms express different genes
(b)
DNA structure impacts gene
expression
(i)
The physical organization of chromatin
makes certain genes available for expression and other genes unavailable
(c)
Many levels of control of
gene expression
(i)
For genes that are available for expression, regulatory opportunities
exist at each step in the pathway from gene to functional protein
(d)
Transcriptional control is
primary means
(i)
Control of transcription is
especially important in determining which genes are expressed
(ii)
In eukaryotes, the selective binding of
transcription factors to enhancer sequences in DNA stimulates
transcription of specific genes
(e)
Control responds to internal
and external cues
(i)
The regulatory activity of some of these DNA-binding proteins is
sensitive to certain hormones and other chemical signals
(f)
See Figure 19.7,
Opportunities for the control of gene expression in eukaryotic cells
(g)
[control of gene expression in
eukaryotes (Google Search)] [index]
(10) Availability
to RNA polymerase
(a)
In general, the less condensed the DNA, the more potentially
available it is to RNA polymerase
(b)
The more available DNA is to RNA polymerase, the more available it is
to transcription
(c)
[transcription RNA polymerase
availability OR access OR accessibility (Google Search)] [index]
(a)
Recall that a methyl group is -CH3
(b)
Methylation of DNA typically consists of a
methylation of the cytosine nitrogenous base
(c)
In general, the more methylated a strand of DNA (i.e., the more
cytosines that are methylated), the less transcriptionally active the DNA
(d)
Methylation thus represents a second, not necessarily independent
modification of DNA (i.e., in addition to condensation) that impacts on transcriptional availability
(e)
[methylation gene expression
(Google Search)] [index]
(12) Transcriptional control of gene expression
(a)
The physical and chemical structure of eucaryotic DNA
impacts on gene expression as outlined above
(b)
Additional controls of transcription
resemble, though do not duplicate the prokaryotic operon model of control of gene expression
(c)
Precisely, gene expression is controlled by protein binding to specific
regions of DNA
(d)
Given structural availability, what genes a eukaryotic
cell expresses typically is controlled, more often than not, by the specific binding
of specific regulatory proteins to specific regions of DNA
(e)
[transcriptional control of
gene expression (Google Search)] [index]
(a)
In addition to introns, a major
difference between eukaryotic and prokaryotic genes is the existence of
sequences called enhancers
(b)
See Figure 19.8, A
eukaryotic gene and its transcript
(c)
[gene anatomy eukaryote or
eukaryotic (Google Search)] [index]
(a)
Enhancers are gene-expression control sequences analogous to
gene-expression control sequences found in prokaryotes
(b)
However, enhancer sequences may be found thousands of bases away from
the reading frame
(c)
The great distance between reading frame and enhancer sequences as well
as the distance between enhancers suggests that enhancer sequences are involved
with changes of DNA structure that serve to enhance transcription
(d)
Particularly, proteins (transcription factors)
bind enhancer sequences thus increasing the transcriptional availability
of a gene
(e)
See Figure 19.9, A model for
enhancer action
(f)
[transcription enhancers
(Google Search)] [index]
(a)
Transcription factors are proteins
that affect transcription by
binding to DNA to facilitate RNA polymerase
binding
(b)
Other transcription factors also bind directly to RNA polymerase,
affecting what promoter sequences the RNA polymerase will bind
(c)
By varying the transcription factors synthesized, a cell can vary what
array of genes are expressed
(d)
In this way cells with metabolically related genes found on many
different chromosomes may be simultaneously transcribed
(e)
I.e., similarly expressed genes would have similar promoters and
enhancer sequences and thus respond similarly to specific arrays of
transcription factors
(f)
See Figure 19.10, Three of
the major types of DNA-binding domains in transcription factors
(g)
[transcription factors
(Google Search)] [index]
(a)
What decides what transcription
factors are synthesized?
(b)
Generally it is internal or environmental influences
(c)
Basically, the cell senses changes in the internal or external
environment and synthesizes or frees up transcription factors in response
(d)
One kind of environmental influence is cell-to-cell chemical signals called hormones
(e)
[environmental influence on
transcription (Google Search)] [index]
(17) Post-transcriptional
control
(a)
While transcription is
the level at which eukaryotic gene expression is
typically controlled, transcription is not the only way that gene
expression may be controlled
(b)
Recall that a gene is not expressed, technically, until its product is
active
(c)
In the case of genes that code for proteins, this means an active protein product
(d)
Note that, additionally, how long a gene function is expressed depends
on how long the various aspects of expression (mRNAs, proteins)
exist prior to their degradation
(e)
Any mechanism of control of gene expression that acts after the
translation of a polypeptide may be termed post-translational control
(f)
See Figure 19.7,
Opportunities for the control of gene expression in eukaryotic cells
(g)
[post-transcriptional control
(Google Search)] [index]
(a)
One way in which the extent of expression of a gene may be controlled
is via mRNA degradation
(b)
The faster mRNAs are destroyed in the cytoplasm, the more temporally linked are transcription and translation
(c)
The more temporally linked transcription and translation, the more
rapidly a cell can respond to its environment via transcription
(d)
This strong temporal linkage between transcription and translation is
how prokaryotes achieve rapid adaptation to environmental cues
(e)
Alternatively, the longer mRNAs last, the more protein synthesis which
may be acquired per mRNA produced, thus reducing some of the cost of protein
synthesis
(f)
[mRNA degradation (Google Search)] [index]
(19) mRNA
activation/inactivation
(a)
mRNAs in eukaryotic cells,
in addition to posttranscriptional modification, typically require activation
via specific protein binding in order for subsequent translation to take place
(b)
This protein binding is another step at which control of gene expression may occur
(c)
For example, whole arrays of mRNAs may be synthesized but not expressed
until a time that is appropriate, such as following the fertilization of an egg
(d)
[mRNA activation, mRNA inactivation (Google Search)] [index]
(a)
Just as with mRNA degradation, a cell may respond to its environment more quickly
by selectively degrading cellular proteins
(b)
Typically degradation involves the recycling of damaged proteins into
constituent amino acids
(c)
By assuring that proteins are turned over with time, a cell is able to
change its phenotype to better match environmental
conditions
(d)
See Figure 19.12,
Degradation of a protein by a protesome
(e)
[protein degradation
(Google Search)] [index]
(21) Protein
activation/inactivation
(a)
A less permanent, and more rapid means of changing phenotype via a modification of protein expression is the
simple activation of and inactivation of cellular proteins
(b)
In this way a cell can avoid wasting proteins
(i.e., destroying proteins that may soon be needed) while simultaneously
rapidly adapting to environmental cues
(c)
It is via protein activation and inactivation that eukaryotic cells achieve their more-rapid cellular adaptation
to environmental conditions
(d)
[protein activation,
protein inactivation
(Google Search)] [index]
(a)
Availability
to RNA polymerase
(b)
Chromatin
(d)
Control of gene expression in eukaryotes
(e)
Enhancers
(g) Euc