Important words and concepts from Chapter 19, Campbell et al., 1999 (3/11/02):

by Stephen T. Abedon (abedon.1@osu.edu) for Biology 113 at the Ohio State University

 

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(1) Chapter title: Genome Organization and Expression in Eukaryotes

(a)                    [genome organization and expression in eukaryotes (Google Search)] [index]

 

HIERARCHICAL EUCARYOTE DNA STRUCTURE

 

(2) Structure of DNA

(a)                    DNA in eukaryotic 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]

(3) Chromatin (see also chromatin)

(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

(c)                    These proteins are called histones

(d)                   Higher levels of organization share the descriptive term, chromatin

(e)                    See Figure, Levels of chromatin packing

(f)                     [chromatin (Google Search)] [index]

(4) Histones (nucleosome) (see also histones and 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]

(5) Euchromatin (see also euchromatin)

(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, Levels of chromatin packing

(c)                    Euchromatin is potentially available for transcription

(d)                   [euchromatin (Google Search)] [index]

(6) Heterochromatin (see also heterochromatin)

(a)                    More tightly packed (condensed) interphase DNA is called heterochromatin

(b)                   See Figure, 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]

(7) Chromosomes (see also chromosome)

(a)                    The ultimate level of chromosome condensation is achieved during prophase/prometaphase

(b)                   See Figured, Levels of chromatin packing

(c)                    The DNA within chromosomes is generally unavailable for transcription

(d)                   [chromosomes (Google Search)] [index]

 

CONTROL OF EUCARYOTE GENE EXPRESSION

 

(8) Plasticity of phenotypes

(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 (see also control of gene expression in eukaryotes)

(a)                    Control of gene expression in eukaryotes occurs at many different levels:

(i)                     Different cells, different genes expressed

      The various cell types of a multicellular organism express different genes

(ii)                   DNA structure impacts gene expression

      The physical organization of chromatin makes certain genes available for expression and other genes unavailable

(iii)                 Many levels of control of gene expression

      For genes that are available for expression, regulatory opportunities exist at each step in the pathway from gene to functional protein

(iv)                 Transcriptional control is primary means

      Control of transcription is especially important in determining which genes are expressed

      In eukaryotes, the selective binding of transcription factors to enhancer sequences in DNA stimulates transcription of specific genes

(v)                   Control responds to internal and external cues

      The regulatory activity of some of these DNA-binding proteins is sensitive to certain hormones and other chemical signals

(b)                   See Figure, Opportunities for the control of gene expression in eukaryotic cells

(c)                    [control of gene expression in eukaryotes (Google Search)] [index]

 

TRANSCRIPTIONAL CONTROL OF GENE EXPRESSION

 

(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]

(11) Methylation (see also methylation)

(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 eukaryotic 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]

(13) Eukaryotic gene anatomy

(a)                    In addition to introns, a major difference between eukaryotic and prokaryotic genes is the existence of sequences called enhancers

(b)                   See Figure, A eukaryotic gene and its transcript

(c)                    [gene anatomy eukaryote or eukaryotic (Google Search)] [index]

(14) Enhancers (see also enhancer)

(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, A model for enhancer action

(f)                     [transcription enhancers (Google Search)] [index]

(15) Transcription factors (see also transcription factor)

(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, Three of the major types of DNA-binding domains in transcription factors

(g)                    [transcription factors (Google Search)] [index]

(16) Environmental influence

(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]

 

POST-TRANSCRIPTIONAL CONTROL OF GENE EXPRESSION

 

(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, Opportunities for the control of gene expression in eukaryotic cells

(g)                    [post-transcriptional control (Google Search)] [index]

(18) mRNA degradation (see also mRNA degradation)

(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]

(20) Protein degradation

(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, Degradation of a protein by a proteasome

(e)                    [protein degradation (Google Search)] [index]

(21) Protein activation/inactivation (see also protein activation)

(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 rapid cellular adaptation to environmental conditions

(d)                   [protein activation, protein inactivation (Google Search)] [index]

 

VOCABULARY

 

(22) Vocabulary [index]

(a)                    Availability to RNA polymerase

(b)                    Chromatin

(c)                    Chromosomes

(d)                   Control of gene expression in eukaryotes

(e)                    Enhancers

(f)                     Environmental influence

(g)                    Eukaryotic gene anatomy

(h)                    Euchromatin

(i)                      Heterochromatin

(j)                      Histones

(k)                    Methylation

(l)                      mRNA activation/inactivation

(m)                  mRNA degradation

(n)                    Nucleosome

(o)                    Plasticity of phenotypes

(p)                    Post-transcriptional control

(q)                    Protein activation/inactivation

(r)                     Protein degradation

(s)                     Structure of DNA

(t)                     Transcription factors

(u)                    Transcriptional control of gene expression

 

Chapter 19, Bio 113 questions:

 

(#) The interaction of DNA with proteins called __________ distinguishes the double helical structure of DNA from that of chromatin.

 

A: Histones

 

(#) As DNA becomes increasingly condensed, __________ of that DNA becomes less and less possible. Because of this, increased structure of DNA within eukaryotic cells is considered to negatively influence gene expression. (note: I am looking for a term which is narrower in meaning than "express" or "gene expression")

A: Transcription

 

(#) Differences in gene expression between eukaryotic cells found within the same organism may be attributed to differences in the array of DNA (and RNA polymerase)-binding proteins called __________ that are contained within a given cell. This means that control of gene expression by eukaryotes differs mechanistically from the employment of operons by prokaryotes.

 

A: transcription factors

 

(#) Which means of protein regulation generally allows the most rapid phenotypic adaptation?

(i)                     mRNA degradation

(ii)                   mRNA activation/inactivation

(iii)                 Protein activation/inactivation

(iv)                 Protein degradation

(v)                   Transcriptional control

 

A: (iii) Protein activation/inactivation

 

(#) What do enhancers found within eukaryotic cells enhance?

 

A: Eukaryotic gene transcription/gene expression

 

(#) In terms of chromatin structure, what is a common means by which control of gene expression is effected? That is, what general chromatin state of being correlates with less gene expression? With more gene expression?

 

A: Generally, more-condensed DNA (heterochromatin) is less available to RNA polymerase and therefore less-well expressed, whereas less condensed DNA (euchromatin) is more available to RNA polymerase and therefore expressed to a greater degree

 

(#) Nucleosomes are complexes of DNA and __________ (a specific category of basic nuclear proteins).

 

A: Histones

 

(#) The expression of nuclear genes is controlled primarily at the level of __________.

(i)                     mRNA modification

(ii)                   Ribosome binding

(iii)                 Protein degradation

(iv)                 Transcription

(v)                   Translation

 

A: (iv) Transcription

 

(#) True or False, unlike prokaryotes, the primary means of control of gene expression in eukaryotes is at the level of translation.

 

A: False (transcription)

 

(#) In general, in what way is the expression of eukaryote genes affected (i.e., increased versus decreased) by methylation of DNA?

 

A: methylation of DNA decreases the level of expression of affected genes

 

(#) Eukaryote transcription factors bind to DNA to facilitate the binding of what enzyme?

(i)                     DNA polymerase

(ii)                   Helicase

(iii)                 Primase

(iv)                 RNA polymerase

(v)                   Topoisomerase

 

A: (iv) RNA polymerase

 

(#) Distinguish Euchromatin from Heterochromatin.

 

A: Heterochromatin is more-fully condensed than euchromatin

 

(#) Which is the more-rapid route to cell-level phenotypic change?

(i)                     Methylation

(ii)                   mRNA degradation

(iii)                 Protein activation/inactivation

(iv)                 Protein degradation

(v)                   Transcriptional control over gene expression

 

(iii) Protein activation/inactivation

 

(#) True or False, by requiring activation before translation, synthesized mRNAs may be stored unused until a time that is appropriate for their use [such as mRNA storage within eggs (ova) for use following fertilization (zygote formation)].

 

A: True

 

(#) True or false, DNA methylation in eukaryotic organisms enhances transcription.

 

A: False

 

(#) Why do histone proteins contain numerous positive charges?

 

A: They employ these positive charges to bind to the negatively charged DNA

 

(#) Which is less available for transcription?

(i)                     Euchromatin

(ii)                   Heterochromatin

(iii)                 Both are equally available for transcription

(iv)                 Neither is available for transcription

 

A: (ii) Heterochromatin

 

(#) In general, in eukaryotes, gene expression is controlled by __________ binding to specific regions of DNA.

(i)                     Enhancer

(ii)                   Inducer

(iii)                 Operon

(iv)                 Protein

(v)                   RNA

 

A: (iv) Protein

 

(#) True or False, eukaryote mRNAs typically must be activated prior to their translation.

 

A: True

 

(#) In general, the more methylated a strand of DNA (i.e., the more cytosines that are methylated), the __________ transcriptionally active the DNA.

(i)                     Less

(ii)                   More

(iii)                 Neither (since methylation has no impact on transcription)

(iv)                 Both (since the impact of methylation on transcription is context dependent)

 

A: (i) Less

 

(#) True or False, protein binding to mRNA in eukaryotic cells is often required for subsequent translation to take place.

 

A: True

 

(#) In what fundamental way can enhancer sequences in eukaryotes differ from gene-expression control DNA sequences found in prokaryotes?

 

A: Enhancer sequences may be found thousands of bases away from affected reading frames

 

(#) True or False, it is methylation primarily of adenine and guanine bases of DNA in eukaryotic systems that can impact transcriptional availability of that DNA.

 

A: False

 

(#) True or False, heterochromatin is less available for transcription compared with euchromatin.

 

A: True

 

(#) By varying the __________ factors synthesized, a cell can vary what array of genes are expressed. In this way cells with metabolically related genes found on many different chromosomes may be simultaneously expressed.

 

A: Transcription