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BMS1062 BIO > TOPIC III Gene Expression and translation > Flashcards

TOPIC III Gene Expression and translation Flashcards

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1
Q

The Rho protein is involved in the _____ stage of transcription.

A

Termination

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2
Q

Which of the following is correct regarding sigma factor?

A

It recognises the promoter sequence

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3
Q

Which of the following occurs first in transcription?

A

Formation of a haloenzyme

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4
Q

What is a haloenzyme?

A

Enzyme activated by a cofactor

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5
Q

Unwinding of the DNA during transcription is the result of the activity of a helicase enzyme downstream of the RNA polymerase. (True or false)

A

False

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6
Q

The RNA transcript being produced by the RNA polymerase is complementary to the template strand of the DNA. (True or False)

A

True

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7
Q

What are features that are common to all tRNA synthetases?

A
  • Active site catalysing the covalent attachment of amino acids to tRNAs
  • Binding surface for the tRNA anticodon
  • Binding site for ATP
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8
Q

Where are promoters for Ecoli genes located?

A

35 bp and 10 bp upstream of first transcribed base

-35 and -10 are separated by 15 to 17 bp) - same side of double helix (important for RNA polymerase to recognise them

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9
Q

What are the two forms of prokaryotic RNA polymerase in initiation?

A

Core enzyme (5 subunits) and the Holoenzyme (core and the sigma factor subunit)

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10
Q

What occurs at the RNA polymerase structure in prokaryotes?

A

One side of sigma factor binds to -35 and -10 regions of promoter on DNA - other side forms interactions with other subunits
- DNA is unwound around -10 region and one strand fed into the channel in RNA polymerase -goes all the way though and incerperates the Mg2+ ion in active site. `

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11
Q

What dos the sigma factor ‘tell’ the RNA polymerase ?

A

Helps it to read the signals in the DNA that tell it where to begin -recognises the -35 and -10 regions

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12
Q

What is the function of 2 alpha subunits (protein) in RNA polymerase?

A
  • Help with enzyme assembly, promote interactions with regulatory proteins
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13
Q

What is the function of the beta subunit in RNA polymerase (prokaryotes)?

A

Catalytic centre

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14
Q

What is the function of the beta prime subunit?

A

Binds DNA

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15
Q

What is the function of the omega subunit?

A

Enzyme assembly, REGULATION OF GENE EXPRESSION

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16
Q

What is the function of the sigma 70 subunit?

A

Binds -10 and -35 regions in promoter and helps separate the DNA strands - creates the transcription bubble by melting DNA

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17
Q

What is the sequence of RNA molecule the same as?

A

The coding strand (except for T because it is replaced by U)

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18
Q

Does RNA polymerase read in the 5’–> 3’ or vice verse?

A

It READS in 3’–> 5’ (moving right to left) and then it SYNTHESISES from 5’–>3’

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19
Q

Which protein is needed for the sigma factor to form an open complex with the RNA polymerase (activator protein)

A

The NtrC protein- binds to enhancer sequence -causes a loop to form where it can then bind to RNA polymerase to cause gene to go over promoter sequence and then SWITCHES GENE ON

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20
Q

When has transcription officially begun?

A

When the gene is SWITCHED ON

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21
Q

What are the two types of terminators in trsnscription ?

A

Intrinsic terminators and Rho dependent terminator sequence

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22
Q

What occurs in Intrinsic terminators?

A

When RNA polymerase recognises instability in the A-U bonds, the RNA sequence terminates and RNA falls off template

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23
Q

How come intrinsic termination just leads to RNA simply ‘falling off’ the template?

A

Due to the RNA strand being in a hairpin loop structure- normally it would go back and fix in linear strcutre BUT loop acts as a roadblock so it can;t go back to fix…it just drops off

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24
Q

Which strand is the hairpin loop formed?

A

On the NEWLY SYNTHESISED STRAND!

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25
Q

What occurs in Rho dependent termination?

A
  • After RNA polymerase has transcribed RUT sequence (row utilisation sequence)
  • Complemenatry sequence of RUT is created on RNA molecule
  • This is recognised by the Rho protein
  • Then wraps around the protein and is a helicase (also tries to catch up with RNA polymerase -Rho moving along RNA whilst RNA polymerase moving along DNA
  • RNA polymerase gets to termination sequence, and pauses…..Rho catches up and unwinds RNA-DNA complex at transcription bubble…RNA, Rho, polymerase ALL FALL OFF
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26
Q

How does Rho unwind the RNA-DNA complex?

A

By hydrolysing ATP

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27
Q

What is the Rho dependent terminator sequence rich in?

A

ONLY C’S (not Gs) before the acutal site of termination

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28
Q

How many possible codons are there in the genetic code?

A

64 possible codons

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29
Q

How many possible reading frames are there and what is a reading frame defined by?

A
  1. (in one direction)g frame gives .
    - Each reading frame gives different sequency of codons
    - only one encodes correct protein
    - other ones not likely to encode proteins
    - an INITIATION codon –> AUG encodes methionine (MET)
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30
Q

What are the possible termination codons?

A

UAA ,UAG, UGA

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31
Q

What does the degenerancy in the genetic code mean?

A

That more than 1 codon can specify an amino acid

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32
Q

Where is the genetic code NOT UNIVERSAL?

A

In mitochondria (codes for Tryp instead of STOP (UGA( )

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33
Q

How many codons specify amino acids?

A

61 , because 3 are STOP codons

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34
Q

Where is the code ambiguous?

A

Where AUG can code for either Met and Start (pretty much unambiguous though)

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35
Q

What is the process of matching amino acids with codons facilitated by?

A 
Carrier molecules (tRNA) (adaptors- bind specific AA and codon) 
- Ribosomes acting as the strucutral network
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36
Q

Which strucuture and process does Crick;s adaptor hypothesis correspond to?

A

The transfer RNA with the amino acids and codon (translation)

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37
Q

What did Hiagland and Zamecnik discover in 1956?

A

Amino acids were activated before incorporated into proteins (attachment of aa to RNA molecule called tRNA to form aminoacyl tRNA)
- tRNA 1st adaptor molecule and tRNA syntherases 2nd adaptor molecules

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38
Q

What actually occurs when amino acids are attached to tRNA?

A

tRNA synthetase attaches aa (by covalent bond) to tRNA (ATP used)
- Forms covalently bonded aminoacyl tRNA

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39
Q

What are tRNAs?

A
  • small chemical modified RNAs (75-90 nucleotides)
  • Unusual bases from chemical modification
  • Have a tridimensional shape
  • H bonds from same internal base pairing
  • Have an adaptor function connecting aas, mRNA and ribosome
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40
Q

`What position do the amino acids attach in the tRNA molecule?

A

3’ end where the molecule looks like an ‘arm’ stretching out on right hand side

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41
Q

Which enzyme matches amino acid with tRNA?

A

aminoacyl tRNA synthetases

- usually 20 different enzymes specific to each of the 20 aas

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42
Q

Can many aminoacyl tRNA synthetases recognise their own tRNA molecules using anticodons?

A

YES! But this is NOT ALWAYS THE CASE

  • Seine-6 diff codons (degenerate)
  • tRNA also recognised using segments on acceptor end and bases elsewhere in molecule
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43
Q

What happens when some organisms don’t have genes for all the 20 aminoacyl tRNA synthetases?

A

They still use all 20 aas to construct their proteins,

- Use enzymes to modify existing structures to get the correct form

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44
Q

How many mistakes do tRNA synthetases make?

A

1 in 10 000

45
Q

What is the second active site in aminoacyl tRNA synthetases for?

A

To perform editing reaction (1 in 3000 error now)

46
Q

What is common to ALL tRNA synthetases?

A
  • Active site catalysing covalent attachment of amino acids to tRNAs
  • Binding surface for tRNA anticodon
  • Binding site for ATP
47
Q

What does the anticodon arm contain?

A

Unusual base called inosine (modified from adenosine)

48
Q

Whst is the tRNA loaded with amino acid called and what is it catalysed by?

A

Charged tRNA and catalysed by aminoacyl-tRNA synthetase

49
Q

What provides energy for making the peptide bond?

A

The ‘permanent’ covalent bond in the tRNA

50
Q

What are the steps in amino acid activation?

A
  • AA attaches to the phosphate on adenine (alpha carboxyl attacks alpha phosphate)
  • ATP then hydrolysed and amino acyl AMP formed
  • AMP group then released an high energy bond is formed
  • this leaves the amino acid part to bond to tRNA -catalysed by amino acyl tRNA synthetase
51
Q

How does amino acyl trRNA synthetase make sure that it is targeting the correct anticodon?

A

‘grabs’ the anticodon and separates it

52
Q

Do all synthetases have proofreading activity?

A

NO!! Some do but not all

53
Q

What is the overall reaction equation for activation of amino acids?

A

Amino acid + tRNA+ ATP —> 2Pi

54
Q

What type of interaction do the codon and anticodon have?

A

Antiparallel orientation from complementary pairing

55
Q

How do tRNAs read the mRNA?

A

By DIRECT interaction

56
Q

Which base of the anticodon is involved i the wobble base pair rule?

A

Base pair 1 because it has the weakest bond (NOTE: bp 1 of ANTICODON in lecture diagram appears on the right hand side- not left)

57
Q

Which orientaton do you have the codon in to show the codon/anticodon relationship?

A

5’–>3’

58
Q

What is the degeneracy of the genetic code due to?

A

Partly due to the nature of the anticodon binding- wobble theory

59
Q

What is the wobble binding?

A
  • Some codon/anticodon interactions can tolerate a mistmatch at the 3’ base of codon (5’ of anticodon) whcih is called wobble
  • doesn’t allow genetic code to be ambiguous (Can read more than one codon specifying same aa)
  • DIffernt wobble base pairs can bind to different anticodon bases
60
Q

What does the wobble allow?

A

Alanine codons GCA, GCC and GCU to all be recognised by the same tRNA

61
Q

How many tRNAs are needed for 61 codons?

A

Only 31 tRNAs

62
Q

What does elongation factor Ts and Tu do?

A

Elongation factor Ts charges Tu with GTP so it is ready to deliver a new tRNA to the ribosome

63
Q

Which units are prokaryotic ribosomes made form?

A

50s and 30s units

64
Q

Which units are eukaryotic ribosomes made from?

A

60s and 40s

65
Q

Are prokaryotic or eukarytotic ribosomes smaller?

A

Prokaryotic

66
Q

How does ribosomal RNA bind to mRNA in prokaryotes?

A
  • Through a ribosome binding site (RBS)

- It is the 16s RNA of ribosome that binds

67
Q

How does ribosomal RNA bind to the mRNA in eukaryotes and which section of ribosome binds?

A
  • Through mRNA at the 5’ cap end

- 18s RNA of rRNA binds

68
Q

What does the large subunit rRNA catalyse?

A
  • Peptide bond formation
69
Q

What are the general steps in translation?

A
  1. Binding of mRNA to small ribosomal subunit
  2. Binding of initiation tRNA at AUG (tRNAiMet in prokarytoes)
  3. Assembly of the complete initiation complex
70
Q

What does initiation in prokaryotes involve?

A
  • IF is the initiaion factor
  • Prokaryotes carry a special form of the of methianinie (N methianine)
  • Shine-balgano sequence binds on mRNA to 16s rRNA
71
Q

According to leningher, what arethe 3 specific steps of initiation of translation in prokaryotes?

A
  1. 30s subunit binds IF1 and IF3 then the mRNA
  2. IF2-GTP binds the 30 s subunit and recruits fMet-tRNA (fmet)—-> base pairs wirth start codon
  3. 50s subunit associates, IF2 hydrolyses GTP and IF1, IF2 and IF3 dissociate, leaving 70s initiation complex
72
Q

What is eIF (initiation of translation) ?

A

It is the eukaryotic initiation factor and has the same role as IF2; forms complex with initiator tRNAi(met) and complex binds to the P site of the small rRNA subunit

73
Q

In eukaryotes, what binds both ends of the mRNA in initation of translation?

A

Complex of eIFs
- eIF4E binds 5’ cap
eIF4g binds poly(A) tail

74
Q

Why do a complex of eIFs bind to the mRNA?

A
  • To ensure the integrity of the mRNA molecule
75
Q

In initiation of translation, what occurs after GTP–> GDP?

A

eIF2 falls off

76
Q

What occurs in the elongation cycle of translation? (4 steps)

A
  1. Binding of amino acyl tRNA (charged tRNA)
  2. Peptide bond formation
  3. Translocation of ribosome
  4. Release of de-acylated tRNA
77
Q

What is the A site in ribosomes?

A

Where the peptide bond is formed

78
Q

What is the A site for in the ribosome subunit?

A

Receptor site

79
Q

What is the E site for in the ribosome complex?

A

Exit site

80
Q

What switches the ribosome back to the normal state after the peptide bond has been formed?

A
  • EGF-G (elongation factor G) hydrolyses GTP to GDP +Pi

then (EF-tu breaks off)

81
Q

Where does the aminoacyl tRNA bind the ribosome?

A

In the A site as a complex with EF-Tu (GTP)

82
Q

What dos the formation of a bond require?

A
  • Peptidyl transferase activity of the ribosome

- When the peptide bond is formed, aminoacyl bond is released

83
Q

Is there any other type of RNA where the peptide bond is formed?

A

NO! Exclusively rRNA

84
Q

What specifically occurs in translocation (3rd step in elongation)?

A
  • After peptide bond is formed…
  • binding of elongation factor is E to the A site is coupled to the conformation change required for translocation to take place
    (aminoacyl tRNA moves to the A site and tRNA carrying the growing polypeptide chain moves to the P site
85
Q

What occurs in the termination of translation?

A
  • Stop codon reached (UAG)
  • Protein release factor binds to stop codon (peptidotransferase adds H2O molecule to aminoacyltransferase
  • at some time ribosome and tRNA DISSOCIATE
86
Q

What are the 4 simple steps of termination of translation?

A
  1. STOP codon
  2. Release factor
  3. Deacylation (release from the last RNA)
  4. Dissociation of the ribosome
87
Q

Which error rate is the highest out of transcription, translation and replication?

A

Transcription and translation hade much higher error rate than replication because of redundancy in code.

88
Q

How do some antibiotics work?

A

By blocking events in transltion

89
Q

How come human ribosomes are unaffected in antibiotics?

A

Strucutral differences b/w human ribosomes and prokaryotes

BUT some antibiotics harm eukaryotes such as chloramphenicol

90
Q

What is the action of chloromycetin?

A

The formation of peptide bonds is inhibited

91
Q

What is the concept of polyribosomes?

A
  • ribosomes work in a production line
  • more than one ribosome moves along a chain at a time
  • simultaneous translation of mRNA by multiple ribosomes
92
Q

Why is eukaryote polysome circular?

A
  • eIFs (bind to the 5’ cap and poly A tail)

- This allows the ribosome machinery to check integrity (if mRNA broken, then won’t have caps and won’t encode)

93
Q

What is spaciotemporal regualtion?

A
  • In prokaryotes everything will happen simultaneously because there is no nucleus BUT in eukaryotes, there is nucleus so must travel out; spatially separated
94
Q

Where is the shine del gano sequence present in intiation of translation?

A

Only in prokaryotes and helps the ribosome to bind (ribososme binding site)

95
Q

What are some post translational modifications in prokaryotes?

A

( possible chemical)

  • Removal of formyl group on fMet
  • aa modifications (less diverse compared to eukaryotes)
96
Q

What are some post translational modifications in eukaryotes?

A

Large number of chemical modifications

  • proteolytic maturation (propeptide removal)
  • complex folding process (chaperone assisted, disulphide bonds)
  • aa modifications (phosphorylation)
97
Q

Where are desitnations for newly translated polypeptides in eukaryotic cells?

A
  1. Finish and release to organelles

2. Stall translation and translocate to ER

98
Q

In eukaryotic cells, where are the polypeptides synthesised?

A

In the cytoplasm (ribosomes in cytoplasm)

99
Q

Do all polypeptides fold spontaneously?

A

Not all, some need to be folded by chaperones (big protein complexes)

100
Q

What is a postranslation modification that occurs to the polypeptide?

A

Addition of amino acids such as ubiquitin (one or multiple units)

101
Q

What is the function of a proteosome?

A

It is a protein complex that degrades the polypeptides when they are not needed
- (ATP driven)

102
Q

What happens in alzheimers and parkingsons with proteosomes?

A

The proteosomes do not recognise that a protein has correct folding when it should’ve…

103
Q

What are the limitations of microarrays?

A
  • Only shows issues at the mRNA level not the protein level
  • You need prior knowledge of sequences of the gene you want to identify (so if you haven’t sequenced a gene you can’t study it)
104
Q

What is true about a microarray?

A

It is a slide attached with high density array of immobilized DNA oligomers representing entire genome of species under study

  • Each DNA oligomer is spotted on the slide and serves as a probe for binding to a unique complementary DNA (cDNA)
  • Most commonly used DNA profiling method
105
Q

What is a conditional/facultative gene?

A
  • Controlled as transcription is needed
106
Q

What is a constitutive gene?

A
  • Transcribed continually
107
Q

What is MicroRNA and Small Interfering RNAs (siRNAs) important for?

A
  • Inhibiting mRNA translation (silencing genes)
  • ## Form a RISC (RNA-Induced Silencing Complex)
108
Q

Where can glycosylatyion and disulfide bond formation occur ?

A
  • In the ER

BMS1062 BIO (7 decks)

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