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Biochem > Ch. 7: RNA and the Genetic Code > Flashcards

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)

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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

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3
Q

defn + func: central dogma of molecular biology

A

lays out the major steps involved in the transfer of genetic info

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4
Q

diagram: flow of genetic info from DNA to protein

A
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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

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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)

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7
Q

what are the 3 main types of RNA found in cells?

A

mRNA
tRNA
rRNA

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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

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9
Q

what happens to mRNA prior to leaving the nucleus? (2)

A
  1. transcribed from template DNA strands by RNA polymerase enzymes in the nucleus of cells
  2. mRNA may then undergo a host of posttranscriptional modifications prior to its release from the nucleus
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10
Q

what is the only type of RNA that contains information that is translated into proteins?

A

mRNA

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11
Q

how is mRNA translated into proteins? (1 sentence)

A

it is read in 3-nucleotide segments (codons)

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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

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13
Q

is mRNA in eukaryotes mono or polycistronic? what about in prokaryotes?

A

eukaryotes = monocistronic
prokaryotes = polycistronic

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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

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15
Q

what does each tRNA molecule contain?

A

a folded strand of RNA that includes a three-nucleotide anticodon

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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

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17
Q

how do amino acids become part of a nascent polypeptide in the ribosome?

A

they are connected to a specific tRNA molecule

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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

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19
Q

where is mature tRNA found?

A

in the cytoplasm

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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

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21
Q

where does the amino acid bind to tRNA?

A

a CCA nucleotide sequence that each mRNA has

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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

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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

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24
Q

what do many rRNA molecules function as?

A

ribozymes

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25
Q

defn: ribozyme

A

enzymes made of RNA molecules instead of peptides

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26
Q

if a gene sequence is a “sentence” describing a protein, then what is a “word”?

A

its basic unit is a three-letter “word” = the codon which is translated into an amino acid

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27
Q

how many bases are in a codon? how many codons are there?

A

there are 3 bases in each codon

there are 64 codons

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28
Q

char (2): codon

A
  1. written in the 5’ –> 3’ direction
  2. each codon is specific for one and only one amino acid
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29
Q

each codon is specific for one and only one amino acid, but is each amino acid only represented by one codon?

A

no, most amino acids are represented by multiple codons

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30
Q

there are 3 codons that do not code for an amino acid, what do these encode for?

A

the termination of translation

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31
Q

what amino acid does every preprocessed eukaryotic protein start with?

A

methionine!

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32
Q

defn + func: start codon vs. stop codons

A

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

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33
Q

how do stop codons work?

A

there are no charged tRNA molecules that recognize these codons, which leads to the release of the protein from the ribosome

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34
Q

mnemonic: stop codons

A

UAA = U Are Annoying
UGA = U Go Away
UAG = U Are Gone

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35
Q

what does that it mean that the genetic code is degenerate?

A

more than one codon can specify a single amino acid

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36
Q

what 2 amino acids are NOT encoded by multiple codons?

A
  1. methionine
  2. tryptophan
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37
Q

defn + func + when does it occur: wobble position

A

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

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38
Q

what are mutations in the wobble position typically called? (2) what is implied by these names?

A
  1. silent
  2. degenerate

there is no effect on the expression of the amino acid and thus no adverse effects on the polypeptide sequence

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39
Q

why will a mutation within an intro usually not change the protein sequence?

A

introns are cleaved out of the mRNA transcript prior to translation

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40
Q

defn: point mutation

A

a mutation that occurs and affects one of the nucleotides in a codon

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41
Q

defn: expressed mutations

A

point mutations that can affect the primary amino acid sequence of the protein

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42
Q

what are the 2 categories of expressed mutations?

A
  1. missense
  2. nonsense
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43
Q

defn: missense mutation

A

a mutation where one amino acid substitutes for another

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44
Q

defn + aka: nonsense mutation

A

a mutation where the codon now encodes for a premature stop codon

aka: truncation mutation

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45
Q

defn: reading frame

A

the three nucleotides of a codon

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46
Q

defn: frameshift mutation

A

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

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47
Q

are the effects of frameshift mutations the same as those of point mutations? what does it depend on?

A

NO, frameshift mutations are typically more serious

heavily depends: where within the DNA sequence the mutation actually occurred

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48
Q

diagram: comparisons of mutations in DNA

A
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49
Q

defn: transcription

A

the creation of mRNA from a DNA template

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50
Q

what does transcription result in?

A

a single strand of mRNA synthesized from the template strand of DNA (antisense strand)

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51
Q

mnemonic: transcription vs. translation

A

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

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52
Q

what is RNA synthesized by?

A

a DNA-dependent RNA polymerase

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53
Q

how does RNA polymerase locate genes?

A

by searching for specialized DNA regions known as promoter regions

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54
Q

func: RNA polymerase II

A

the main player in transcribing mRNA in eukratyoes

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55
Q

defn + name origin: TATA box

A

the binding site of RNA polymerase II in the promoter region

name: high concentration of thymine and adenine bases

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56
Q

func: transcription factors

A

help the RNA polymerase locate and bind to this promoter region of the DNA, helping to establish where transcription will start

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57
Q

does RNA polymerase require a primer to start generating a transcript?

A

no

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58
Q

what are the 3 types of RNA polymerases in eukaryotes? (where are they located, what do they do)

A

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

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59
Q

direction: RNA polymerase movement

transcription

A

RNA polymerase travels along the template strand 3’–>5’

transcribed mRNA constructed in the 5’–>3’ direction

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60
Q

does RNA polymerase proofread?

A

no, the synthesized transcript will not be edited

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61
Q

role of coding strand (sense strand) of DNA in transcription (2)

A
  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
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62
Q

numbering system used to identify the location of important bases in the DNA strand (5)

A
  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
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63
Q

diagram: transcription of DNA to hnRNA

A
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64
Q

at what point will transcription terminate? what happens after this?

A

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)

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65
Q

func: hnRNA

A

mRNA is derived from hnRNA via posttranscriptional modifications

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66
Q

what are the 3 types of post-transcriptional processing? + diagram

A
  1. intron/exon splicing
  2. 5’ cap
  3. 3’ poly-A tail
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67
Q

what is the main purpose behind post-transcriptional processing?

A

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

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68
Q

analogy: hnRNA and post-transcriptional processing

A

nucleus = happy home of the cell

DNA strands = caregivers

hnRNA = child

child must mature in order to survive

69
Q

mnemonic: intron vs. exon

A

INtrons stay IN the nucleus

EXons will EXit the nucleus as part of the mRNA

70
Q

what + why: splicing of introns and exons

A

included in the maturation of hnRNA

splicing of the transcript to remove noncoding sequences (introns) and ligate coding sequences (exons) together

71
Q

what does splicing?

A

spliceosome

72
Q

process (3): splicing

A
  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
Q

what + process (3) + func: 5’cap

A

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
Q

what + char (2) + func (2): 3’ Poly-A Tail

A

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
Q

analogy: poly-A tail

A

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
Q

at what point is the mRNA mature? where can mature mRNA go?

A

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
Q

where will untranslated regions of mRNA still exist even with mature mRNA and why do these exist?

A

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
Q

defn + additional func (2) + diagram: alternative splicing

A

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
Q

what is an advantage of alternative splicing?

A

an organism can make many more different proteins from a limited number of genes

80
Q

func: nuclear pores

A

the mature mRNA transcript exits the nucleus through these

81
Q

what happens to mRNA once in the cytoplasm?

A

it finds a ribosome to begin translation

the anticodon of the tRNA binds to the codon on the mature mRNA in the ribosome

82
Q

defn: translation

A

converting the mRNA transcript into a functional protein

83
Q

what are the 5 things that translation requires?

A
  1. mRNA
  2. tRNA
  3. ribosomes
  4. amino acids
  5. energy (as GTP)
84
Q

what is it composed of + char (2) + func: ribosome

A

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
Q

what are the A, P, and E sites in ribosome? (overall and each)

A

the three binding sites for tRNA

A site = aminoacyl

P site = peptidyl

E site = exit

86
Q

summary of 5’ –> 3’ and terminology for DNA to RNA to protein

A

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
Q

what does the “S” value mean in the names of rRNA? how is it determined?

A

the size of the strand

determined experimentally by studying the behavior of particles in a centrifuge

88
Q

how many strands of rRNA do eukaryotic ribosomes contain? + what are they named

A

4

  1. 28S
  2. 18S
  3. 5.8S
  4. 5S
89
Q

RNA polymerase I transcribes the 28S, 18S, and 5.8S rRNAS as ____ within ____ which results in ______

A

as a SINGLE UNIT within the NUCLEOLUS which results in a 45S RIBOSOMAL PRECURSOR RNA

90
Q

what does the 45S pre-RNA become?

A

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
Q

what does RNA polymerase III transcribe? where does this happen?

A

transcribes the 5S rRNA (found in the 60S ribosomal subunit)

this takes place outside the nucleolus

92
Q

defn: ribosomal subunits vs. ribosome

A

ribosomal subunits created: 60S and 40S

join together during protein synthesis to form: whole 80S ribosome

93
Q

subunits + ribosome + diagram: prokaryotic vs. eukaryotic

A

EUK: 60S + 40S = 80S

PROK: 50S + 30S = 70S

94
Q

why are the subunit numbers not additive to the ribosome number?

A

each subunits numbers’ are based on size and shape, not size alone

95
Q

do transcription and translation occur at the same time or different times?

A

PROK: ribosomes start translating before the mRNA is complete

EUK: transcription and translation occur at separate times and locations within the cell

96
Q

what are the 3 stages of translation? + diagram

A
  1. initiation
  2. elongation
  3. termination
97
Q

what 2 things are required for each step of translation?

A
  1. specialized factors (IF initiation factors, EF elongation factors, RF release factors)
  2. GTP
98
Q

steps (3): initiation

A
  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
Q

where on the mRNA does the small ribosomal subunit bind to? (pro + euk)

A

PRO: binds to the Shine-Dalgarno sequence in the 5’ untranslated region of the mRNA

EUK: binds to the 5’ cap structure

100
Q

what is the initial amino acid? (pro + euk)

A

PRO: N-formylmethionine (fMet)

EUK: methionine

101
Q

defn: elongation

A

a 3-step cycle that is repeated for each amino acid added to the protein after the initiator methionine

102
Q

process: elongation

A
  1. the ribosome moves 5’ to 3’ along the mRNA, synthesizing the protein from its amino (N-) to carboxyl (C-) terminus
103
Q

what happens with the A site? (2)

A
  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
Q

what happens with the P site? (5)

A
  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
Q

what happens with the E site? (2)

A
  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
Q

mnemonic: order of sites in the ribosome during translation

A

APE

107
Q

func: elongation factors (EF)

A

assist by locating and recruiting aminoacyl-tRNA along with GTP, while helping to remove GDP once the energy has been used

108
Q

func: signal sequences

A

designate a particular destination for the protein

109
Q

what is the function of a signal sequence for peptides that will be secreted, like hormones and digestive enzymes?

A

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
Q

where do other signal sequences direct proteins to? (3)

A
  1. nucleus
  2. lysosomes
  3. cell membrane
111
Q

process (4): termination

A
  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
Q

what must happen to the nascent polypeptide before it becomes a functioning protein?

A

subject to posttranslational modifications

113
Q

what are 4 types of posttranslational processing and which one is an essential step for the final synthesis of the protein?

A
  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
Q

defn + func: chaperones

A

a specialized class of proteins

func: to assist in the protein-folding process

115
Q

modification by cleavage events: one example?

how does this work for peptides with signal sequences?

A

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
Q

classic example: subunits come together for peptides with quaternary structure

A

hemoglobin

117
Q

what are the 4 types of posttranslational modification that involve other biomolecules that are added to the peptide?

A
  1. phosphorylation
  2. carboxylation
  3. glycosylation
  4. prenylation
118
Q

defn: phosphorylation

A

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
Q

defn: carboxylation

A

addition of carboxylic acid groups, usually to serve as calcium-binding sites

120
Q

defn: glycosylation

A

addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination

121
Q

defn: prenylation

A

addition of lipid groups to certain membrane-bound enzymes

122
Q

defn + analogy: operon

A

a cluster of genes transcribed as a single mRNA

a simple on-off switch for gene control in prokaryotes

122
Q

what is the overall function of the regulatory processes governing gene expression in prokaryotes?

A

rules that are necessary in determining which subset of genes are selectively expressed or silenced in the prokaryotic cell

123
Q

defn: trp operon

A

five genes in E. coli encode for enzymes that manufacture the amino acid tryptophan and are arranged in a cluster on the chromosome

124
Q

func: Jacob-Monod model

A

used to describe the structure and function operons

125
Q

what do 4 things do operons contain according to the Jacob-Monod model?

A
  1. structural genes
  2. an operator site
  3. a promoter site
  4. a regulator gene
126
Q

func: structural gene

A

codes for the protein of interest

127
Q

defn + location in relation to structural gene: operator site

A

func = a nontranscribable region of DNA that is capable of binding a repressor protein

upstream of the structural gene

128
Q

func + location in relation to the operator site: promoter site

A

provides a place for RNA polymerase to bind

upstream of the operator site

129
Q

func + location in relation to the promoter site: regulator gene

A

codes for a protein known as the repressor

furthest upstream

130
Q

what are the 2 types of operons?

A
  1. inducible systems
  2. repressible systems
131
Q

how do inducible systems work? (2) + summary + diagram

A
  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
Q

defn: negative control mechanisms (inducible systems are an example)

A

the binding of a protein reduces transcriptional activity

133
Q

how is the way inducible systems operate analogous to competitive inhibition for enzyme activity?

A

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
Q

why are inducible systems useful?

A

they allow gene products to be produced only when they are needed

135
Q

what is a classic example of an inducible system?

A

the lac operon which contains the gene for lactase

136
Q

why is the lac operon necessary and what induces it? (3) + diagram

A
  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
Q

what is the lac operon assisted by?

A

binding of the catabolite activator protein (CAP)

138
Q

defn + func: catabolite activator protein (CAP)

A

a transcriptional activator used by E. coli when glucose levels are low to signal that alternative that alternative carbon sources should be used

139
Q

defn: positive control mechanisms

A

the binding of a molecule increases transcription of a gene

140
Q

how is CAP induced? (2)

A

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
Q

summary: negative control vs. positive control

inducible system vs. repressible system

A

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
Q

defn + diagram: repressible systems

A

continually allow constant production of a protein product/gene transcription unless a corepressor binds to the repressor to stop transcription

143
Q

how do repressible systems work? (2)

A
  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
Q

how do repressible systems tend to serve as negative feedback? (2)

A
  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
Q

what is a classic example of a negative repressible system?

A

the trp operon

146
Q

how does the trp operon work? (3)

A
  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
Q

defn: transcription factors

A

transcription-activating proteins that search the DNA looking for specific DNA-binding motifs

148
Q

what are the 2 recognizable domains that transcription factors tend to have?

A
  1. a DNA-binding domain
  2. an activation domain
149
Q

func: DNA-binding domain

A

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
Q

defn: DNA response element

A

a sequence of DNA that binds only to specific transcription factors

151
Q

func: activation domain

A

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
Q

defn: cis regulators vs. trans regulators

A

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
Q

what can happen once the transcription complex is formed?

A

basal (low-level) transcription can begin and maintain moderate, but adequate, levels of the protein encoded by this gene in the cell

154
Q

in what situations might expression need to be increased? (3)

what is the aka for increased?

how is this accomplished by eukaryotic cells? (2)

A

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
Q

defn + func: enhancer

A

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
Q

what are the receptors that correspond to

cAMP

cortisol

and estrogen

A

cAMP = cyclic AMP response element-binding protein (CREB)

cortisol = the glucocorticoid receptor

estrogen = estrogen receptor

157
Q

diagram: stimulation of transcription by an enhancer and its associated transcription factors

A
158
Q

where are enhancer regions located?

how is this different from the upstream promoter elements

A
  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
Q

what is a benefit of using enhancer regins?

A

genes have an increased likelihood to be amplified because of the variety of signals that can increase transcription levels

160
Q

what are the 2 methods of gene duplication and what is the effect of gene duplication?

A

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
Q

what is DNA packaged as in eukaryotic cells and what is required for this to happen?

A

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
Q

defn: heterochromatin vs. euchromatin

A

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
Q

func + defn: histone acetylases

A

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
Q

what effect does acetylation of histone proteins have?

A

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
Q

diagram + summary: chromatin remodeling by acetylation

A

increases space between histones, allowing better access to DNA for transcription factors

166
Q

defn + func: histone deacetylases

A

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
Q

func: DNA methylases

A

add methyl groups to cytosine and adenine nucleotides

methylation of genes is often linked with the silencing of gene expression

168
Q

are heterochromatin or euchromatin regions of the DNA heavily methylated and what effect does this have?

A

heterochromatin

hindering access of the transcriptional machinery to the DNA

Biochem (12 decks)

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