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eukaryotic gene expression Flashcards

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1
Q

what is transcription?

A

the process by which a complementary RNA copy is made under the direction of the template strand of a specific region of the DNA molecule, catalysed by the enzyme RNA polymerase

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2
Q

transcription

what is the function of the promoter?

A

the promoter, containing the TATA box and the transcription start site, is located immediately upstream of the gene. the TATA box serves as a binding site for a general transcription factor, which facilitates the binding of RNA polymerase

the promoter is not transcribed except for the transcription start site

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3
Q

in what order is the template DNA strand read?

A

the template DNA strand is read in the 3’ to 5’ direction.

DNA is SYNTHESISED in the 5’ to 3’ direction

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4
Q

what is the difference between the template (non-coding) strand and the non-template (coding) strand?

A

the template strand is the DNA strand that is transcribed, while the non-template strand is not transcribed.
the sequence on the template strand is complementary to that of the RNA, while the sequence on the non-template strand is exactly the same as the RNA but the thymine in DNA is replaced by uracil in RNA

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5
Q

what is a gene?

A

a gene is a section of DNA that encodes information in the form of a specific base sequence to direct the synthesis of one polypeptide chain or RNA molecule.
it is a unit of inheritance located in a fixed position (locus) on the chromosome which specifies a particular character of an organism

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6
Q

what are the 3 key components of a gene?

A

the promoter, the coding region and the termination sequence

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7
Q

what does the promoter (part of a gene) contain?

A

the TATA box and the transcription start site

the transcription start site is where RNA synthesis begins. the transcription start site is also the only part of the promoter that is transcribed.

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8
Q

what is the purpose of the TATA box?

A

the TATA box serves as a binding site for a general transcription factor, which facilitates the binding of RNA polymerase.

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9
Q

in what direction does RNA polymerase read the DNA template?

A

RNA polymerase reads the DNA template in the 3’ to 5’ direction

RNA is synthesised in the 5’ to 3’ direction

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10
Q

how does RNA polymerase synthesise RNA?

A

RNA polymerase reads the DNA template in the 3’ to 5’ direction, catalysing the assembly of ribonucleotides, forming complementary base pairs with the template. RNA polymerase also catalyses the formation of phosphodiester bonds between the free 5’ phosphate group of the incoming ribonucleotide/NTP and the free 3’ hydroxyl group of the growing RNA polynucleotide chain

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11
Q

what is the termination sequence?

A

the termination sequence is found at the end of a gene and it codes for a polyadenylation signal sequence (AAUAAA) in pre-mRNA. the whole termination sequence is transcribed, resulting in transcription termination

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12
Q

what do general transcription factors do?

A
  1. position RNA polymerase correctly at the promoter
  2. release RNA polymerase from the promoter to begin elongating the RNA against the DNA template once transcription has begun.
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13
Q

what are the 3 stages of transcription?

A

initiation, elongation & termination

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14
Q

step 1 of initiation (transcription)

how is the transcription initiation complex formed?

A
  • general transcription factors are assembled along the promoter.
  • TFIID (a GTF) binds to the TATA box found within the promoter
  • GTFs mediate the binding of RNA polymerase to the promoter, forming the complex known as the transcription initiation complex.
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15
Q

step 2 of initiation (transcription)

how does the DNA helix unwind & separate?

A
  • binding of RNA polymerase to the promoter causes the DNA double helix to unwind and the 2 strands separate
  • hydrogen bonds between complementary base pairs are disrupted
  • a transcription bubble is created
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16
Q

step 3 of initiation (transcription)

how are ribonucleotides assembled?

A
  • 1 of the 2 exposed DNA strands acts as a template for complementary base pairing to direct the assembly of incoming ribonucleotides (NTPs)
  • RNA polymerase catalyses the formation of the first phosphodiester bond
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17
Q

step 1 of elongation (transcription)

how does the transcription bubble move?

A
  • as the RNA polymerase moves along the template DNA in the 3’ to 5’ direction, the DNA double helix continues to transiently unwind
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18
Q

step 2 of elongation (transcription)

how is the polynucleotide elongated during the elongation stage of transcription?

A
  • ribonucleotides form complementary base pairs with the DNA template
  • as each ribonucleoside triphosphate is brought in, its 2 terminal phosphates are removed
  • the remaining free 5’ phosphate group is added to the free 3’ hydroxyl group of the growing RNA chain via the formation of a phosphodiester bond catalysed by RNA polymerase

mRNA is synthesised in the 5’ to 3’ direction

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19
Q

stage 3 of elongation (transcription)

how is DNA re-annealed and proofread during transcription?

A
  • RNA polymerase reanneals the unwound DNA behind it, dissociating the growing RNA chain from the template
  • RNA polymerase carries out proofreading functions and is responsible for the removal of any incorrectly inserted ribonucleotide

RNA polymerase can carry out proofreading, UNLIKE DNA polymerase which cannot (used in DNA replication)

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20
Q

termination (transcription)

what happens during the termination stage of transcription?

A
  • transcription proceeds until after the RNA polymerase transcribes a termination sequence in the DNA, which triggers the release of the RNA chain and the dissociation of the RNA polymerase
  • the transcribed termination sequence codes for a polyadenylation signal sequence
  • RNA polymerase continues transcription until at a point about 10 to 35 nucleotides down stream of the polyadenylation signal sequence
  • the cleavage site is also the site of addition of poly(A) tail
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21
Q

what are the 3 post-transcriptional modifications?

A
  1. addition of 5’ methylguanosine cap
  2. RNA splicing
  3. addition of 3’ poly(A) tail
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22
Q

what is a 5’ methylguanosine cap?

A

the 5’ end of the new RNA molecule is modified by the addition of a ‘cap’ that consists of a methylated guanine nucleotide/methylguanosine triphosphate

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23
Q

what are the purposes of the 5’ methylguanosine cap?

A
  1. protects mRNA from degradation by hydrolytic enzymes
  2. defines the 5’ end of the mRNA, which serves to recruit the small subunit of the ribosome for translation initiation
  3. distinguishes mRNAs from other types of RNA molecules
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24
Q

what happens during RNA splicing?

A

introns are removed while the remaining exons are spliced/joined together. this requires the hydrolysis of ATP

splicing is carried out by a spliceosome. splicing will be covered further in control of ege.

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25
Q

what is a 3’ poly(A) tail?

A

after the pre-mRNA is cleaved by an endonuclease after the AAUAAA polyadenylation sequence,
the 3’ end of the mRNA is modified by adding a series of approximately 200 adenine nucleotides.
this is catalysed by the enzymes poly(A)-polymerase

26
Q

what are the functions of the 3’ poly(A) tail?

A
  1. protects the mRNA from degradation by nucleases, making the mRNA a more stable template for translation in the cytoplasm
  2. required to facilitate the export of mRNA out of the nucleus
27
Q

what are the 3 stop codons?

A

UAA
UAG
UGA

28
Q

what is the start codon and what amino acid does it code for?

A

AUG
Met

29
Q

TUNDWP

what are the features of the genetic code?

A

Triplet
Universal
Non-overlapping
Degenerate
Wobble base phenomenon
Punctuation codons

30
Q

what does the genetic code being a triplet code mean?

A

each mRNA codon that specifies an amino acid in a polypeptide chain consists of three nucleotide bases

31
Q

what does the genetic code being (almost) universal mean?

A

the same code is used by almost all organisms

32
Q

what does the genetic code being non-overlapping and continuous mean?

A
  • each codon is read as a triplet in the 5’ to 3’ direction. nucleotides in mRNA are read continuously, as successive groups of 3 nucleotides, one codon at a time without skipping any nucleotides
  • there can be 3 possible reading frames for every mRNA sequence since the genetic code is read in blocks of 3 nucleotides
33
Q

what does the genetic code being degenerate but unambigious mean?

A
  • a single amino acid can be coded by more than one different codon
  • only 2 amino acids are coded for by a single codon each, methionine (AUG) and tryptophan (UGG)
  • every codon codes just for one amino acid so the code is unambigious
  • most amino acids are encoded by degenerate codons that differ in the 3rd position of the codon
34
Q

what is the wobble base phenomenon?

A
  • some tRNA can recognise 2 or more of the degenerate codons. eg tRNA with the anticodon AAG recognises not only the complementary mRNA codon UUC but also UUU
  • this is called a wobble
  • this suggests that the base-pairing at the 3rd base is not so specific, so a change in the 3rd base by a mutation may still permit the correct incorporation of a given amino acid in a polypeptide (silent mutation)
35
Q

what are the punctuation codons of the genetic code?

A
  • start codon AUG codes for methionine
  • defines the first amino acid of the polypeptide chain AND the reading frame used from that point on
  • 3 stop codons UAA, UAG, UGA are stop signals mark the end of protein synthesis
  • they do not code for any amino acid and there is no tRNA with an anticodon complemntary to these 3 codons.
36
Q

what is translation?

A

translation is the process in which a polypeptide chain is synthesised by ribosomes using genetic information encoded in mature mRNA template

37
Q

what are the 3 stages of translation?

A

initiation, elongation & termination

38
Q

what is mature mRNA?

A

mature mRNA is obtained after pre-mRNA undergoes post-transcriptional modifications which includes adding a 5’ cap, a 3’ poly(A) tail and RNA splicing

mature mRNA consists of 2 regions: the protein-coding region (codons representing a.a. sequence of polypeptide + start & stop codon) and the untranslated regions (precede the start codon - leader sequence - and follow the stop codon - trailer sequence)

39
Q

what are the roles of mature mRNA?

A
  1. mature mRNA serves as an intermediate that carries the copy of DNA sequence information that encodes proteins.
  2. mature mRNA acts as a template for translation
40
Q

what are the roles of tRNA

A
  1. tRNA serves as an adaptor molecule in the translation of an mRNA nucleotide sequence into the amino acid sequence of a polypeptide
  2. tRNA is used to bring in specific amino acids in a sequence corresponding to the sequence
41
Q

why can tRNA act as an adaptor?

A
  1. tRNA’s anticodon is able to determine the specific amino acid attached to the CCA stem
  2. tRNA’s anticodon is able to form complementary base pairs with the mRNA codon
42
Q

how do amino acids attach to the 3’ end (CCA stem) of a tRNA molecule?

A
  • the 3D structure of tRNA is recognised by the enzyme aminoacyl-tRNA synthetase that catalyses the formation of an ester linkage (bc of the 3’ OH end) between the CCA stem and the specific amino acid
  • when a tRNA has its 3’ CCA stem attached to the amino acid corresponding to its anticodon, it is called an aminoacyl-tRNA
43
Q

the enzyme responsible is called aminoacyl-tRNA synthetase

how is aminoacyl-tRNA (amino acid + tRNA) formed?

A
  1. cells produce 20 different synthetase enzymes, one for each of the 20 distinct amino acids.
  2. each of the 20 different synthetase enzymes must recognise the specific anticodon on a tRNA AND a specific amino acid.
  3. each of the 20 different synthetase enzyme covalently attaches a specific amino acid to the 3’ CCA stem of its appropriate set of tRNA molecules via an ester linkage, forming aminoacyl-tRNA. this reaction requires the hydrolysis of ATP
  4. the active site of each aminoacyl-tRNA synthetase must be complementary to the 3D conformation of the specific amino acid AND specific anticodon sequence of the tRNA in order to bind
  5. the resulting aminoacyl-tRNA is released from the synthetase enzyme and delivers its amino acid to a growing polypeptide chain on a ribosome
44
Q

what are the purposes of rRNA (ribosomal RNA)?

A
  1. rRNA forms the core of the ribosome - it is the main constituent of the A and P sites and of the interface between the large and small ribosomal units
  2. rRNA in the large ribosomal unit has peptidyl transferase activity, catalysing the formation of peptide bonds between amino acids
45
Q

what is the function of each ribosome subunit?

A
  • the small subunit contains an mRNA binding site, where the mRNA binds.
  • the large subunit has 3 binding sites for tRNA (A, P and E site)
46
Q

what are the 3 binding sites for tRNA and their functions?

A
  • A site (aminoacyl-tRNA site) - holds the incoming tRNA carrying the next amino acid to be added
  • P site (peptidyl-tRNA site) - holds the tRNA carrying the growing polypeptide chain
  • E site (exit site) - site of release of the deacylated tRNA (tRNA without amino acid attached)
47
Q

what are the roles of ribosomes?

A
  1. ribosomes provide an environment for specific recognition between a codon of mRNA and an anticodon of tRNA
  2. the ribosome holds the tRNA and mRNA in close proximity, positioning the new amino acid for addition to the growing polypeptide
  3. rRNA in the large ribosomal subunit has peptidyl transferase activity, catalysing the formation of peptide bonds between amino acids

ribosomes translate in the 5’ to 3’ direction

48
Q

what are the 3 types of translation factors?

translation factors are proteins

A
  1. initiation factors - for assembly of mRNA, first tRNA and ribosomal subunits
  2. elongation factors - for synthesis of polypeptide chains
  3. release factors - for recognition of the stop codon and disassembly of the translation machinery
49
Q

step 1 of initiation of translation

how are initiation factors binded to the small subunit?

A
  • eukaryotic initiation factors (eIFs) bind to the small subunit of a ribosome and position the initiator tRNA, tRNAimet, which carries a methionine to its P site
  • this step requires GTP
50
Q

step 2 of initiation of translation

how is the small subunit binded to mRNA?

A
  • the small subunit binds to the mRNA by recognising the 5’-methylguanosine cap
  • the small subunit then moves downstream in the 5’ to 3’ direction along the mRNA in search of the start codon AUG, which signals the start of translation
51
Q

step 3 of initiation of translation

how is the initiation complex formed?

A
  • the anticodon on the initiator tRNA (tRNAimet) associates with the start codon on mRNA (AUG) through complementary base pairing
  • methionine is always the first amino acid in a newly formed polypepide as the initiator tRNA has a unique anti-codon loop that is distinct from that of the tRNA that normally carries methionine
  • eIFs (eukaryotic initiation factors) dissociate with the hydrolysis of GTP, allowing the large ribosomal subunit to bind, completing a eukaryotic 80s translation initiation complex
  • the initiator tRNA sits in the P site of the ribosome and the initial methionine forms the N terminus of the polypeptide
  • the A site is vacant as it is waiting for the entry of the next aminoacyl-tRNA complementary to the second codon of the mRNA
52
Q

step 1 of elongation & translocation of translation

how does aminoacyl-tRNA bind to the A site?

A
  • aminoacyl-tRNA carrying the 2nd amino acid in the chain binds to the ribosomal A site via complementary base pairing between its anticodon and the codon in the mRNA exposed at the A site.
  • the codon-anticodon interaction is held in place by hydrogen bonds
  • tRNAs are brought in by elongation factors. energy is expended with the hydrolysis of GTP
53
Q

step 2 of elongation & translocation of translation

how is a peptide bond formed between amino acids?

A
  • when the 2nd tRNA is bound to the ribosome, its amino acid is placed directly adjacent to the initial methionine
  • peptidyl transferase in the large ribosomal unit catalyses the formation of a peptide bond between the carboxyl end of methionine and the amino group of the 2nd amino acid
  • methionine is transferred to the 2nd amino acid carried by the aminoacyl-tRNA at the A site
  • the ester bond between the initial methionine and tRNA is broken to release the initial methionine
  • the deacylated tRNA lies in the P site, while the new peptidyl-tRNA has been created in the A site
54
Q

step 3 of elongation & translocation of translation

how is the ribosome translocated?

A
  • the ribosome is translocated one codon (3 nucleotides) at a time in the 5’ to 3’ direction, guided by elongation factors
  • hydrolysis of GTP is required to provide energy
  • this relocates the initial deacylated tRNA to from the P site to the E site, where it diffuses out of the ribosome
  • this repositions the peptidyl-tRNA from the A site to the P site, and
  • exposes the next codon on the mRNA at the A site. this continues until a stop codon is encountered at the A site.
55
Q

termination of translation

how does termination occur?

A
  • termination occurs when a stop codon (UAA, UAG, UGA) in the mRNA reaches the A site of the ribosome. these codons don’t code for amino acid but signal to stop translation
  • a protein called a release factor binds directly to the stop codon in the A site
  • the release factor causes the addition of a water molecule instead of an amino acid to the polypeptide chain, freeing the carboxyl end of the completed polypeptide from tRNA in the P site by hydrolysis
  • the polypeptide is released through the exit tunnel of the large ribosomal subunit
  • the ribosome then releases the mRNA (which can be reused) and separates into the large and small subunits
  • tRNA molecules may then be recycled and use to form new aminoacyl-tRNA
56
Q

what are polyribosomes/polysomes?

A
  • polyribosomes/polysomes are ribosomes that occur as clusters. they simultaneously translate polypeptides from the same mRNA strand
  • as soon as the preceding ribosomes has translated a portion of the nucleotide sequence, the 5’ end of the mRNA is associated with a new ribosome. each ribosome in the polysome independently synthesises a single polypeptide during its translation of the mRNA sequence
  • this is advantageous as more polypeptide molecules can be made in a given time
57
Q

what are the differences in function for free ribosomes and bound ribosomes?

A
  • free ribosomes are suspended in the cytoplasm and synthesise proteins that dissolve in and exert their effects in the cytosol (cytosolic proteins)
  • bound ribosomes are attached to the cytoplasmic side of the endoplasmic reticulum and synthesise targetted proteins to be secreted from the cell

polypeptides of proteins destined for the endomembrane system or for secretion are marked by a signal peptide, which targets the polypeptides to the ER

58
Q

what are the 4 post-translational modifications of polypeptides?

A
  1. attaching it to biochemical functional groups
  2. making structural changes (eg forming disulfide linkages)
  3. removing a sequence of amino acids (proteolytic cleavage)
  4. attaching ubiquitin
59
Q

what biochemical functional groups could be attached to proteins in the post-translational modifications?

A
  1. acetate, methyl, phosphate, various lipids and carbohydrates may be attached
  2. glycosylation (adding specific short-chain carbohydrates) is common in membrane proteins
  3. reverse phosphorylation for signal transduction
60
Q

what does ubiquitin do?

A
  • ubiquitin marks proteins for proteolysis by the proteasome

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