Ch. 7: RNA and the Genetic Code Flashcards
1
Q
what is the genetic code used for and why?
A
to translate the genetic information of DNA and RNA (coded using nitrogenous bases) into proteins (made of amino acids, a very different language)
2
Q
what is the main difference in the role between nucleotides and proteins in the preservation and development of species across generations?
A
NUCLEOTIDES = play a crucial role in maintaining our genetic identity from generation to generation
PROTEINS = that help organisms develop and perform the necessary functions of life
3
Q
defn + func: central dogma of molecular biology
A
lays out the major steps involved in the transfer of genetic info
4
Q
diagram: flow of genetic info from DNA to protein
A
5
Q
what direction is mRNA synthesized in? what is the relationship between the mRNA and DNA?
A
synthesized: 5’ –> 3’
complementary and antiparallel to the DNA template strand
6
Q
what direction is the mRNA translated in? what translates it? what happens simultaneously?
A
5’ –> 3’ direction
ribosome translates mRNA
as it synthesizes the protein from the amino terminus (N-terminus) to the carboxy terminus (C-terminus)
7
Q
what are the 3 main types of RNA found in cells?
A
mRNA
tRNA
rRNA
8
Q
defn + func: mRNA
A
defn: messenger RNA
func: carries the information specifying the amino acid sequence of the protein to the ribosome = the messenger of genetic information
9
Q
what happens to mRNA prior to leaving the nucleus? (2)
A
- transcribed from template DNA strands by RNA polymerase enzymes in the nucleus of cells
- mRNA may then undergo a host of posttranscriptional modifications prior to its release from the nucleus
10
Q
what is the only type of RNA that contains information that is translated into proteins?
A
mRNA
11
Q
how is mRNA translated into proteins? (1 sentence)
A
it is read in 3-nucleotide segments (codons)
12
Q
defn: monocistronic vs. polycistronic
A
monocistronic = each mRNA molecule translates into only one protein product
polycistronic = starting the process of translation at different locations in the mRNA can result in different proteins
13
Q
is mRNA in eukaryotes mono or polycistronic? what about in prokaryotes?
A
eukaryotes = monocistronic
prokaryotes = polycistronic
14
Q
defn + func + diagram: tRNA
A
defn: transfer RNA
func: responsible for converting the language of nucleic acids to the language of amino acids and peptides
15
Q
what does each tRNA molecule contain?
A
a folded strand of RNA that includes a three-nucleotide anticodon
16
Q
func: anticodon in tRNA
A
recognizes and pairs with the appropriate codon on an mRNA molecule while in the ribosome
the orientation of this interaction is antiparallel because base-pairing is involved
17
Q
how do amino acids become part of a nascent polypeptide in the ribosome?
A
they are connected to a specific tRNA molecule
18
Q
what are the tRNA molecules attached to amino acids to become part of a nascent polypeptide called?
A
charged or activated with an amino acid
19
Q
where is mature tRNA found?
A
in the cytoplasm
20
Q
func + required for use + what does this imply: aminoacyl-tRNA synthetase
A
a different one of these activates each type of amino acid (the aminoacyl-tRNA synthetase transfers the activated amino acid to the 3’ end of the correct tRNA)
requires: 2 high-energy bonds from ATP –>
implies that the attachment of the amino acid is an energy rich bond
21
Q
where does the amino acid bind to tRNA?
A
a CCA nucleotide sequence that each mRNA has
22
Q
what is the high-energy aminoacyl-tRNA bond used for?
A
to supply the energy needed to create a peptide bond during translation
23
Q
defn + func (3) + where is it synthesized: rRNA
A
defn: ribosomal RNA
synthesized: in the nucleolus
func: 1. as an integral part of the ribosomal machinery used during protein assembly in the cytoplasm
2. helps catalyze the formation of peptide bonds
3. is important in splicing out its own introns within the nucleus
24
Q
what do many rRNA molecules function as?
A
ribozymes
25
defn: ribozyme
enzymes made of RNA molecules instead of peptides
26
if a gene sequence is a "sentence" describing a protein, then what is a "word"?
its basic unit is a three-letter "word" = the codon which is translated into an amino acid
27
how many bases are in a codon? how many codons are there?
there are 3 bases in each codon
there are 64 codons
28
char (2): codon
1. written in the 5' --> 3' direction
2. each codon is specific for one and only one amino acid
29
each codon is specific for one and only one amino acid, but is each amino acid only represented by one codon?
no, most amino acids are represented by multiple codons
30
there are 3 codons that do not code for an amino acid, what do these encode for?
the termination of translation
31
what amino acid does every preprocessed eukaryotic protein start with?
methionine!
32
defn + func: start codon vs. stop codons
START = the codon for methionine (AUG) = the start codon for translation of the mRNA into protein
STOP = three codons that encode for termination of protein translation
UGA
UAA
UAG
33
how do stop codons work?
there are no charged tRNA molecules that recognize these codons, which leads to the release of the protein from the ribosome
34
mnemonic: stop codons
UAA = U Are Annoying
UGA = U Go Away
UAG = U Are Gone
35
what does that it mean that the genetic code is degenerate?
more than one codon can specify a single amino acid
36
what 2 amino acids are NOT encoded by multiple codons?
1. methionine
2. tryptophan
37
defn + func + when does it occur: wobble position
when: for amino acids with multiple codons, the first 2 bases are usually the same, and the third base in the codon is variable
defn: the wobble position is this variable third base in the codon
func: an evolutionary development designed to protect against mutations in the coding regions of DNA
38
what are mutations in the wobble position typically called? (2) what is implied by these names?
1. silent
2. degenerate
there is no effect on the expression of the amino acid and thus no adverse effects on the polypeptide sequence
39
why will a mutation within an intro usually not change the protein sequence?
introns are cleaved out of the mRNA transcript prior to translation
40
defn: point mutation
a mutation that occurs and affects one of the nucleotides in a codon
41
defn: expressed mutations
point mutations that can affect the primary amino acid sequence of the protein
42
what are the 2 categories of expressed mutations?
1. missense
2. nonsense
43
defn: missense mutation
a mutation where one amino acid substitutes for another
44
defn + aka: nonsense mutation
a mutation where the codon now encodes for a premature stop codon
aka: truncation mutation
45
defn: reading frame
the three nucleotides of a codon
46
defn: frameshift mutation
occurs when some number of nucleotides are added to or deleted from the mRNA sequence, usually resulting in changes in the amino acid sequence or premature truncation of the protein
47
are the effects of frameshift mutations the same as those of point mutations? what does it depend on?
NO, frameshift mutations are typically more serious
heavily depends: where within the DNA sequence the mutation actually occurred
48
diagram: comparisons of mutations in DNA
49
defn: transcription
the creation of mRNA from a DNA template
50
what does transcription result in?
a single strand of mRNA synthesized from the template strand of DNA (antisense strand)
51
mnemonic: transcription vs. translation
when we TRANSCRIBE information, we use the same language to write it down (like in court)
TRANSLATION: we change the language --> RNA translation changes the language from nucleotides to amino acids
52
what is RNA synthesized by?
a DNA-dependent RNA polymerase
53
how does RNA polymerase locate genes?
by searching for specialized DNA regions known as promoter regions
54
func: RNA polymerase II
the main player in transcribing mRNA in eukratyoes
55
defn + name origin: TATA box
the binding site of RNA polymerase II in the promoter region
name: high concentration of thymine and adenine bases
56
func: transcription factors
help the RNA polymerase locate and bind to this promoter region of the DNA, helping to establish where transcription will start
57
does RNA polymerase require a primer to start generating a transcript?
no
58
what are the 3 types of RNA polymerases in eukaryotes? (where are they located, what do they do)
RNA polymerase I
- in nucleolus
- synthesizes rRNA
RNA polymerase II
- in nucleus
- synthesizes hnRNA (pre-processed mRNA) and some small nuclear RNA (snRNA)
RNA polymerase III
- in nucleus
- synthesizes tRNA and some rRNA
59
direction: RNA polymerase movement
transcription
RNA polymerase travels along the template strand 3'-->5'
transcribed mRNA constructed in the 5'-->3' direction
60
does RNA polymerase proofread?
no, the synthesized transcript will not be edited
61
role of coding strand (sense strand) of DNA in transcription (2)
1. not used as a template during transcription
2. identical to the mRNA transcript except all thymines in DNA have been replaced with uracil in mRNA
62
numbering system used to identify the location of important bases in the DNA strand (5)
1. the first base transcribed from DNA to RNA is the +1 base of that gene region
2. bases to the LEFT of this (upstream, toward 5' end) are NEGATIVE (-1, -2, -3, etc.)
3. bases to the RIGHT (downstream, toward 3' end) are POSITIVE (+2, +3, +4)
4. no nucleotide in the gene is 0
5. the TATA box is usually around -25
63
diagram: transcription of DNA to hnRNA
64
at what point will transcription terminate? what happens after this?
transcription will continue along the DNA coding region until the RNA polymerase reaches a termination sequence or stop signal
after this: the DNA double helix re-forms, and the primary transcript formed is hnRNA (heterogenous nuclear hnRNA)
65
func: hnRNA
mRNA is derived from hnRNA via posttranscriptional modifications
66
what are the 3 types of post-transcriptional processing? + diagram
1. intron/exon splicing
2. 5' cap
3. 3' poly-A tail
67
what is the main purpose behind post-transcriptional processing?
before hnRNA can leave the nucleus and be translated into protein, it MUST undergo these THREE processes to allow it to interact with the ribosome and survive the cytoplasm's condition
68
analogy: hnRNA and post-transcriptional processing
nucleus = happy home of the cell
DNA strands = caregivers
hnRNA = child
child must mature in order to survive
69
mnemonic: intron vs. exon
INtrons stay IN the nucleus
EXons will EXit the nucleus as part of the mRNA
70
what + why: splicing of introns and exons
included in the maturation of hnRNA
splicing of the transcript to remove noncoding sequences (introns) and ligate coding sequences (exons) together
71
what does splicing?
spliceosome
72
process (3): splicing
1. in the spliceosome, small nuclear RNA (snRNA) molecles couple with proteins known as small nuclear ribonucleoproteins (snRNPs)
2. the snRNP/snRNA complex recognizes both the 5' and 3' splice sites of the introns
3. these noncoding sequences are excised in the form of a lariat (lasso-shaped structure) and then degraded
73
what + process (3) + func: 5'cap
what: 7-methylguanylate triphosphate cap
1. added at the 5' end of the hnRNA molecule
2. added during transcription
3. recognized by the ribosome as the binding site
func: protects the mRNA from degradation in the cytoplasm
74
what + char (2) + func (2): 3' Poly-A Tail
what: polyadenosyl (poly-A) tail
1. added to the 3' end of the mRNA transcript
2. composed of adenine bases
func: 1. protects the message against rapid degradation
2. assists with export of the mature mRNA from the nucleus
75
analogy: poly-A tail
as a fuse for a "time bomb" for the mRNA transcript --> as soon as the mRNA leaves the nucleus it will start to get degraded from its 3' end
the longer the poly-A tail, the more time the mRNA will be able to survive before being digested in the cytoplasm
76
at what point is the mRNA mature? where can mature mRNA go?
mature when:
1. only the exons remain
2. the cap and tail have been added
can now be transported into the cytoplasm for protein translation
77
where will untranslated regions of mRNA still exist even with mature mRNA and why do these exist?
UTRs exist at the 5' and 3' edges of the transcript because the ribosome initiates translation at the start codon (AUG) and will end at the stop codon (UAA, UGA, UAG)
78
defn + additional func (2) + diagram: alternative splicing
for some genes in eukaryotic cells, the primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by the same original gene
additional func: 1. regulation of gene expression
2. generating protein diversity
79
what is an advantage of alternative splicing?
an organism can make many more different proteins from a limited number of genes
80
func: nuclear pores
the mature mRNA transcript exits the nucleus through these
81
what happens to mRNA once in the cytoplasm?
it finds a ribosome to begin translation
the anticodon of the tRNA binds to the codon on the mature mRNA in the ribosome
82
defn: translation
converting the mRNA transcript into a functional protein
83
what are the 5 things that translation requires?
1. mRNA
2. tRNA
3. ribosomes
4. amino acids
5. energy (as GTP)
84
what is it composed of + char (2) + func: ribosome
composed of: proteins and rRNA
char: 1. large and small subunits (which only bind together during protein synthesis)
2. structure dictates its function
func: to bring the mRNA message together with the charged aminoacyl-tRNA complex to generate the protein
85
what are the A, P, and E sites in ribosome? (overall and each)
the three binding sites for tRNA
A site = aminoacyl
P site = peptidyl
E site = exit
86
summary of 5' --> 3' and terminology for DNA to RNA to protein
DNA --> DNA = replication = new DNA synthesized 5' to 3'
DNA --> RNA = transcription = new RNA synthesized 5' to 3' (template is read 3' to 5')
RNA --> protein = translation = mRNA read 5' to 3'
87
what does the "S" value mean in the names of rRNA? how is it determined?
the size of the strand
determined experimentally by studying the behavior of particles in a centrifuge
88
how many strands of rRNA do eukaryotic ribosomes contain? + what are they named
4
1. 28S
2. 18S
3. 5.8S
4. 5S
89
RNA polymerase I transcribes the 28S, 18S, and 5.8S rRNAS as ____ within ____ which results in ______
as a SINGLE UNIT within the NUCLEOLUS which results in a 45S RIBOSOMAL PRECURSOR RNA
90
what does the 45S pre-RNA become?
45S is processed to become
the 18S of the 40S (small) ribosomal subunit
the 28S and 5.8S rRNAs of the 60S (large) ribosomal subunit
91
what does RNA polymerase III transcribe? where does this happen?
transcribes the 5S rRNA (found in the 60S ribosomal subunit)
this takes place outside the nucleolus
92
defn: ribosomal subunits vs. ribosome
ribosomal subunits created: 60S and 40S
join together during protein synthesis to form: whole 80S ribosome
93
subunits + ribosome + diagram: prokaryotic vs. eukaryotic
EUK: 60S + 40S = 80S
PROK: 50S + 30S = 70S
94
why are the subunit numbers not additive to the ribosome number?
each subunits numbers' are based on size and shape, not size alone
95
do transcription and translation occur at the same time or different times?
PROK: ribosomes start translating before the mRNA is complete
EUK: transcription and translation occur at separate times and locations within the cell
96
what are the 3 stages of translation? + diagram
1. initiation
2. elongation
3. termination
97
what 2 things are required for each step of translation?
1. specialized factors (IF initiation factors, EF elongation factors, RF release factors)
2. GTP
98
steps (3): initiation
1. the small ribosomal subunit binds to the mRNA
2. the charged initiator tRNA binds to the AUG start codon through base-pairing with its anticodon within the P site of the ribosome
3. the large subunit binds to the small subunit, forming the completed initiation complex, this is assisted by initiation factors (IF) that are not permanently associated with the ribosome
99
where on the mRNA does the small ribosomal subunit bind to? (pro + euk)
PRO: binds to the Shine-Dalgarno sequence in the 5' untranslated region of the mRNA
EUK: binds to the 5' cap structure
100
what is the initial amino acid? (pro + euk)
PRO: N-formylmethionine (fMet)
EUK: methionine
101
defn: elongation
a 3-step cycle that is repeated for each amino acid added to the protein after the initiator methionine
102
process: elongation
1. the ribosome moves 5' to 3' along the mRNA, synthesizing the protein from its amino (N-) to carboxyl (C-) terminus
103
what happens with the A site? (2)
1. holds the incoming aminoacyl-tRNA complex
2. this is the next amino acid that is being added to the growing chain, and is determined by the mRNA codon within the A site
104
what happens with the P site? (5)
1. holds the tRNA that carries the growing polypeptide chain
2. where the first amino acid (methionine) binds because it is starting the polypeptide chain
3. a peptide bond is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site
4. this requires peptidyl transferase (enzyme, part of the large subunit)
5. GTP is used for energy during the formation of this bond
105
what happens with the E site? (2)
1. where the now inactivated (uncharged tRNA) pauses transiently before exiting the ribosome
2. as the now-uncharged tRNA enters the E site, it quickly unbinds from the mRNA and is ready to be charged
106
mnemonic: order of sites in the ribosome during translation
APE
107
func: elongation factors (EF)
assist by locating and recruiting aminoacyl-tRNA along with GTP, while helping to remove GDP once the energy has been used
108
func: signal sequences
designate a particular destination for the protein
109
what is the function of a signal sequence for peptides that will be secreted, like hormones and digestive enzymes?
directs the ribosome to move to the ER so that the protein can be translated directly into the lumen of the rough ER (from there the protein can be sent to the Golgi apparatus and be secreted from a vesicle via exocytosis)
110
where do other signal sequences direct proteins to? (3)
1. nucleus
2. lysosomes
3. cell membrane
111
process (4): termination
1. when any of the 3 stop codons moves into the A site, a protein called release factor (RF) binds to the termination codon
2. this causes a water molecule to be added to the polypeptide chain
3. the addition of water allows peptidyl transferase and termination factors to hydrolyze the completed polypeptide chain from the final tRNA
4. the polypeptide chain will then be released from the tRNA in the P site and 2 ribosomal subunits will dissociate
112
what must happen to the nascent polypeptide before it becomes a functioning protein?
subject to posttranslational modifications
113
what are 4 types of posttranslational processing and which one is an essential step for the final synthesis of the protein?
1. proper folding (essential)
2. modification by cleavage events
3. subunits come together for peptides with quaternary structure
4. other biomolecules may be added to the peptide
114
defn + func: chaperones
a specialized class of proteins
func: to assist in the protein-folding process
115
modification by cleavage events: one example?
how does this work for peptides with signal sequences?
EX: insulin (needs to be cleaved from a larger, inactive peptide to achieve its active form)
peptides with signal sequences: the signal sequence must be cleaved if the protein is to enter the organelle and properly function
116
classic example: subunits come together for peptides with quaternary structure
hemoglobin
117
what are the 4 types of posttranslational modification that involve other biomolecules that are added to the peptide?
1. phosphorylation
2. carboxylation
3. glycosylation
4. prenylation
118
defn: phosphorylation
addition of a phosphate group (PO42-) by protein kinases to activate or deactivate proteins
most commonly seen in eukaryotes with serine, threonine, and tyrosine
119
defn: carboxylation
addition of carboxylic acid groups, usually to serve as calcium-binding sites
120
defn: glycosylation
addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination
121
defn: prenylation
addition of lipid groups to certain membrane-bound enzymes
122
defn + analogy: operon
a cluster of genes transcribed as a single mRNA
a simple on-off switch for gene control in prokaryotes
122
what is the overall function of the regulatory processes governing gene expression in prokaryotes?
rules that are necessary in determining which subset of genes are selectively expressed or silenced in the prokaryotic cell
123
defn: trp operon
five genes in E. coli encode for enzymes that manufacture the amino acid tryptophan and are arranged in a cluster on the chromosome
124
func: Jacob-Monod model
used to describe the structure and function operons
125
what do 4 things do operons contain according to the Jacob-Monod model?
1. structural genes
2. an operator site
3. a promoter site
4. a regulator gene
126
func: structural gene
codes for the protein of interest
127
defn + location in relation to structural gene: operator site
func = a nontranscribable region of DNA that is capable of binding a repressor protein
upstream of the structural gene
128
func + location in relation to the operator site: promoter site
provides a place for RNA polymerase to bind
upstream of the operator site
129
func + location in relation to the promoter site: regulator gene
codes for a protein known as the repressor
furthest upstream
130
what are the 2 types of operons?
1. inducible systems
2. repressible systems
131
how do inducible systems work? (2) + summary + diagram
1. the repressor is bonded tightly to the operator system and thus acts as a roadblock --> RNA polymerase is unable to get from the promoter to the structural gene because the repressor is in the way
2. to remove that block, an inducer must bind the repressor protein so that RNA polymerase can move down the gene
summary: allow for gene transcription only when an inducer is present to bind the otherwise present repressor protein
132
defn: negative control mechanisms (inducible systems are an example)
the binding of a protein reduces transcriptional activity
133
how is the way inducible systems operate analogous to competitive inhibition for enzyme activity?
as the concentration of the inducer increases, it will pull more copies of the repressor off of the operator region, freeing up those genes for transcription
134
why are inducible systems useful?
they allow gene products to be produced only when they are needed
135
what is a classic example of an inducible system?
the lac operon which contains the gene for lactase
136
why is the lac operon necessary and what induces it? (3) + diagram
1. bacteria can digest lactose, but it is more energetically expensive than digesting glucose
2. therefore, bacteria only want to use this option if lactose is high and glucose is low
3. the lac operon is induced by the presence of lactose, so these genes are only transcribed when it is useful to the cell
137
what is the lac operon assisted by?
binding of the catabolite activator protein (CAP)
138
defn + func: catabolite activator protein (CAP)
a transcriptional activator used by E. coli when glucose levels are low to signal that alternative that alternative carbon sources should be used
139
defn: positive control mechanisms
the binding of a molecule increases transcription of a gene
140
how is CAP induced? (2)
falling levels of glucose cause an increase in the signaling molecule cyclic AMP (cAMP), which binds to CAP
this induces a conformational change in CAP that allows it to bind the promoter region of the operon, further increasing transcription of the lactase gene
141
summary: negative control vs. positive control
inducible system vs. repressible system
NEGATIVE = the binding of a protein to DNA stops transcription
POSITIVE = the binding of a protein to DNA increases transcription
INDUCIBLE system = the system is normally "off" but can be made to turn "on" given a particular signal
REPRESSIBLE system = the system is normally "on" but can be made to turn "off" given a particular signal
142
defn + diagram: repressible systems
continually allow constant production of a protein product/gene transcription unless a corepressor binds to the repressor to stop transcription
143
how do repressible systems work? (2)
1. the repressor made by the regulator gene is inactive until it binds to a corepressor
2. this complex then binds the operator site to prevent further transcription
144
how do repressible systems tend to serve as negative feedback? (2)
1. often, the final structural product can serve as a corepressor
2. thus, as its levels increase, it can bind the repressor, and the complex will attach to the operator region to prevent further transcription of the same gene
145
what is a classic example of a negative repressible system?
the trp operon
146
how does the trp operon work? (3)
1. when tryptophan is high in the local environment, it acts as a corepressor
2. the binding of two molecules of tryptophan to the repressor causes the repressor to bind to the operator site
3. thus, the cell turns off its machinery to synthesize its own tryptophan, which is an energetically expensive process because of its easy availability in the environment
147
defn: transcription factors
transcription-activating proteins that search the DNA looking for specific DNA-binding motifs
148
what are the 2 recognizable domains that transcription factors tend to have?
1. a DNA-binding domain
2. an activation domain
149
func: DNA-binding domain
binds to a specific nucleotide sequence in the promoter region or to a DNA response element to help in the recruitment of transcriptional machinery
150
defn: DNA response element
a sequence of DNA that binds only to specific transcription factors
151
func: activation domain
allows for the binding of several transcription factors and other important regulatory proteins, such as RNA polymerase and histone acetylases, which function in the remodeling of the chromatin structure
152
defn: cis regulators vs. trans regulators
CIS regulators = the DNA regulatory base sequences (such as promoters, enhancers, and response elements) because they are in the same vicinity as the gene they control
TRANS regulators = transcription factors because they have to be produced and translocated back to the nucleus --> they travel through the cell to their point of action
153
what can happen once the transcription complex is formed?
basal (low-level) transcription can begin and maintain moderate, but adequate, levels of the protein encoded by this gene in the cell
154
in what situations might expression need to be increased? (3)
what is the aka for increased?
how is this accomplished by eukaryotic cells? (2)
in response to specific signals such as
1. hormones
2. growth factors
3. other intracellular conditions
AMPLIFIED
accomplished through
1. enhancers
2. gene duplication
155
defn + func: enhancer
defn: several response elements may be grouped together to form an enhancer
func: allows for the control of one gene's expression by multiple signals (signal molecules, such as cAMP, cortisol, and estrogen bind to specific receptors, all of which are transcription factors that bind to their respective response elements within the enhancer)
156
what are the receptors that correspond to
cAMP
cortisol
and estrogen
cAMP = cyclic AMP response element-binding protein (CREB)
cortisol = the glucocorticoid receptor
estrogen = estrogen receptor
157
diagram: stimulation of transcription by an enhancer and its associated transcription factors
158
where are enhancer regions located?
how is this different from the upstream promoter elements
1. they can be up to 1000 base pairs away from the gene they regulate
2. they can even be located within an intron (noncoding region)
different from upstream promoter elements, because those must be within 25 bases of the start of the gene
159
what is a benefit of using enhancer regins?
genes have an increased likelihood to be amplified because of the variety of signals that can increase transcription levels
160
what are the 2 methods of gene duplication and what is the effect of gene duplication?
effect: increasing expression of a gene product
1. in series on the same chromosome, yielding many copies in a row of the same genetic info
2. in parallel by opening the gene with helicases and permitting DNA replication only of that gene. this can continue until hundreds of copies of the gene exist in parallel on the same chromosome
161
what is DNA packaged as in eukaryotic cells and what is required for this to happen?
packaged in the nucleus as chromatin
requires chromatin remodeling to allow transcription factors and the transcriptional machinery easier access to the DNA to regulate gene expression levels in the cell
162
defn: heterochromatin vs. euchromatin
heterochromatin = tightly coiled DNA that appears dark under the microscope. the tight coiling makes it inaccessible to the transcription machinery, so these genes are inactive
euchromatin = looser DNA that appears light under the microscope. these are accessible by transcription machinery, so these genes are active
163
func + defn: histone acetylases
coactivators that transcription factors can recruit
func: involved in chromatin remodeling because they acetylate lysine residues found in the amino terminal tail regions of histone proteins
164
what effect does acetylation of histone proteins have?
it decreases the positive charge on lysine residues and weakens the interaction of the histone with DNA, resulting in an open chromatin conformation that allows for easier access of the transcriptional machinery to the DNA and thus potential increased gene expression levels
165
diagram + summary: chromatin remodeling by acetylation
increases space between histones, allowing better access to DNA for transcription factors
166
defn + func: histone deacetylases
proteins that function to remove acetyl groups from histones, which results in a closed chromatin conformation and overall decrease in gene expression levels in the cell (gene silencing)
167
func: DNA methylases
add methyl groups to cytosine and adenine nucleotides
methylation of genes is often linked with the silencing of gene expression
168
are heterochromatin or euchromatin regions of the DNA heavily methylated and what effect does this have?
heterochromatin
hindering access of the transcriptional machinery to the DNA
