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bms2062 > The Central Dogma of Molecular Biology > Flashcards

The Central Dogma of Molecular Biology Flashcards

1
Q

How does mRNA ensure that genetic information is used effeciently?

A
  1. Only necessary genes are active
  2. The amount of gene product is easily controlled and can vary from gene to gene
  3. Distinct proteins can be synthesised from a single gene via mRNA modification (splicing)
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2
Q

An _________________ is defined as a DNA or RNA sequence which contains a run of codons uninterupted by a stop codon

A

An open reading frame (ORF) is defined as a DNA or RNA sequence which contains a run of codons uninterupted by a stop codon

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3
Q

Definition

the loss or gain of a nucleotide causing a shift in the reading frame

A

Deletion/Insertion

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4
Q

What is the optimum loop size of an RNA?

A

7 bases

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5
Q

RNA is synthesised in a __ to __ direction

A

RNA is synthesised in a 5’ to 3’ direction

i.e. is is added at the 3’ end

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6
Q

Define

Central Dogma

A

the two-step process, transcription and translation, by which the information in genes flows into proteins: DNA → RNA → protein.

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7
Q

Define

miRNA

A

a small non-coding RNA molecule

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8
Q

Definition

a DNA or RNA sequence which contains a run of codons uninterrupted by a stop codon. (Or a stretch of codons between two stop codons)

A

Open reading frame (ORF)

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9
Q

Give an example of a positively charged R group

A
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10
Q

Single-stranded RNA can form intra-molecular base-pairs between ______________ to form antiparallel double stranded structures or _________

A

Single-stranded RNA can form intra-molecular base-pairs between inverted repeats to form antiparallel double stranded structures or stem-loops

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11
Q

Definition

A codon that signals the first amino acid to be used in the synthesis of the polypeptide chain of a protein

A

Initiation codon

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12
Q

A stretch of DNA that encodes a protein is called what?

A

Coding sequence

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13
Q

Define

Shine-Dalgano sequence

A

a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG

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14
Q

Definition

the term that refers to the strand used by DNA polymerase or RNA polymerase to attach complementary bases during DNA replication or RNA transcription

A

Template strand

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15
Q

Definition

an enzyme that is responsible for copying a DNA sequence into an RNA sequence, during the process of transcription

A

RNA polymerase

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16
Q

Definition

The single strand of a separated double helix of DNA that has the same base sequence as the MESSENGER RNA (mRNA) formed from the complementary DNA strand

A

Coding strand

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17
Q

The initiation sequence of a prokaryotic mRNA is preceeded by what?

A

Ribosome binding site (Shine-Dalgano sequence)

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18
Q

Definition

relating to or denoting organic compounds in which carbon atoms form open chains (as in the alkanes), not aromatic rings

A

Aliphatic

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19
Q

RNA is produced using which strand of DNA?

A

Template strand

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20
Q

Definition

either of two sections, one on each side of a coding sequence on a strand of mRNA

A

Untranslated regions (UTR)

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21
Q

Define

Substitution

A

a mutation that exchanges one base for another (i.e., a change in a single “chemical letter” such as switching an A to a G)

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22
Q

What are the termination codons?

A

TAA, TAG, TGA

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23
Q

What processes is RNA structure crucial for?

A
  • Transcription, in termination, splicing and transport
  • Regulation of RNA stability
  • Translation, in initiation, elongation, termination and regulation
  • Catalysis
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24
Q

How are the untranslated regions of mRNA important?

A

Untranslated regions provide binding sites for proteins that stabilise, destabilise or transport RNA

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25
Q

What is a tRNA with an attached amino acid called?

A

Aminoacyl or “charged” tRNA

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26
Q

What motifs can signal whether an ORF is part of a real protein coding sequence?

A
  • Promotor
  • Ribosome binding site
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27
Q

Define

Methylguanosine cap

A

a specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA

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28
Q

What is the key to identifying the most likely structure of an RNA?

A

Thermodynamics - the more energy that is released, the more stable the structure (-ve ΔG = stable)

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29
Q

Definition

a small non-coding RNA molecule

A

miRNA

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30
Q

Define

Aliphatic

A

relating to or denoting organic compounds in which carbon atoms form open chains (as in the alkanes), not aromatic rings

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31
Q

Definition

a sequence of three nucleotides forming a unit of genetic code in a transfer RNA molecule, corresponding to a complementary codon in messenger RNA

A

Anticodon

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32
Q

Define

Polyadenylation

A

the addition of a poly(A) tail to a messenger RNA

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33
Q

True or False:

RNA can base pair with DNA or RNA

A

True

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34
Q

Promotor sequences are an example of DNA ______ occurring in many genes, which can be identified through bioinformatic analysis. A ______________ is built using the most commonly found bases at each position in a motif.

A

Promotor sequences are an example of DNA motifs occurring in many genes, which can be identified through bioinformatic analysis. A consensus sequence is built using the most commonly found bases at each position in a motif.

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35
Q

Define

Open reading frame (ORF)

A

a DNA or RNA sequence which contains a run of codons uninterrupted by a stop codon. (Or a stretch of codons between two stop codons)

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36
Q

Give an example of a nonpolar, aliphatic R group

A
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37
Q

What types of RNA are produced in both prokaryotes and eukaryotes?

A

mRNA

rRNA

tRNA

antisense RNA

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38
Q

Definition

a sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule

A

Codon

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39
Q

Define

Motif

A

a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance

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40
Q

What is the initiation codon?

A

ATG - methionine (Met)

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41
Q

Give an example of a polar, uncharged R group

A
42
Q

Define

Gene splicing

A

a post-transcriptional modification in which a single gene can code for multiple proteins

43
Q

Definition

a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG

A

Shine-Dalgano sequence

44
Q

Define

Promotor sequence

A

DNA sequences that define where transcription of a gene by RNA polymerase begins

45
Q

How are the ends of the mRNA modified in eukaryotes?

A

A 7-methylguanosune “cap” is added to the 5’ end

A “tail” of A is added to the 3’ end

46
Q
A
47
Q

True or False:

All coding sequences are ORFs but not all ORFs are coding sequences

A
48
Q

Define

Untranslated regions (UTR)

A

either of two sections, one on each side of a coding sequence on a strand of mRNA

49
Q

Definition

the nucleic acid blueprint for a protein

A

Coding sequence

50
Q

Which bases pair together in RNA?

A

A pairs with U

G pairs with C

G pairs with U

51
Q

What is the minimum amount of amino acids encoded by a ORF needed for you to conclude that it is part of a gene?

A

60 amino acids

52
Q

How many total reading frames are there in double stranded DNA?

A

6 (3 per strand)

53
Q

Give an example of an aromatic R group

A
54
Q

Define

Deletion/Insertion

A

the loss or gain of a nucleotide causing a shift in the reading frame

55
Q

In transcription, the template is always read in direction __ to __

A

In transcription, the template is always read in direction 3’ to 5’

56
Q

The function of tRNAs depends on sequence and ________ structure

A

The function of tRNAs depends on sequence and tertiary structure

57
Q

Define

Consensus sequence

A

a virtual sequence which shows the most commonly found base at each particular position in a motif. In promotors, this can be thought of as the optimal sequence for binding RNA polymerase

58
Q

Define

Termination codon

A

a nucleotide triplet within messenger RNA that signals a termination of translation into proteins

59
Q

Define

Initiation codon

A

A codon that signals the first amino acid to be used in the synthesis of the polypeptide chain of a protein

60
Q
A
61
Q

Definition

DNA sequences that define where transcription of a gene by RNA polymerase begins

A

Promotor sequence

62
Q

Why is prokaryotic mRNA very unstable?

A

There is no modifications made to the 5’ and 3’ ends like in eukaryotes

63
Q

Define

Anticodon

A

a sequence of three nucleotides forming a unit of genetic code in a transfer RNA molecule, corresponding to a complementary codon in messenger RNA

64
Q

By convention, how is an RNA sequence written?

A

Written as texxt in the 5’ to 3’ direction, from left to right

65
Q

What are coding sequences made up of?

A

Open reading frames (ORFs) that contain a start codon and are flanked by regulatory motifs which direct production of RNA

66
Q

Definition

the addition of a poly(A) tail to a messenger RNA

A

Polyadenylation

67
Q

Definition

the two-step process, transcription and translation, by which the information in genes flows into proteins: DNA → RNA → protein.

A

Central Dogma

68
Q

True or False:

An ORF must (almost always) start with a Met, but a coding sequence may start with any anino acid

A

False

A coding sequence must (almost always) start with a Met, but an ORF may start with any anino acid

69
Q

RNA is an exact copy of which of the strands of DNA?

A

Coding strand

70
Q

Define

Reading frame

A

a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets

71
Q

What are the differences between prokaryotic and eukaryotic mRNAs?

A

Eukaryotes - transcription and splicing produces single gene mRNAs (monocistronic); most RNAs are exported from nucleus to function in cytoplasm; multi-use

Prokaryotes - transcription without splicing produces multi-gene mRNAs (polycistronic/operon); one time use

72
Q

True or False:

tRNA has the codon

A

False

tRNA has the anticodon; mRNA has the codon

73
Q

What can repeats in DNA indicate?

A
  • Binding sites for proteins
  • The presence of mobile genetic elements
  • Contribute to single-stranded nucleic acid secondary structure
74
Q

Define

Bioinformatics

A

the collection, classification, storage, and analysis of biochemical and biological information using computers especially as applied in molecular genetics and genomics

75
Q

Give an example of a negatively charged R group

A
76
Q

Definition

a post-transcriptional modification in which a single gene can code for multiple proteins

A

Gene splicing

77
Q

Define

Coding sequence

A

the nucleic acid blueprint for a protein

78
Q

Definition

a nucleotide triplet within messenger RNA that signals a termination of translation into proteins

A

Termination codon

79
Q

What types of RNA are produced in only eukaryotes?

A

microRNA

snRNA

snoRNA

siRNA

80
Q

True or False:

Base pairing in RNA is the same as DNA

A

False

G can also weakly pair with U

81
Q

Define

RNA polymerase

A

an enzyme that is responsible for copying a DNA sequence into an RNA sequence, during the process of transcription

82
Q

Definition

a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets

A

Reading frame

83
Q

What are the steps of annotated a DNA sequence?

A
  1. Analyse sequence and add information on:
  • Transcripts encoded
  • Proteins encoded
  • Binding sites for machinery
  • Evolution
  1. Research scientific literature for experimental data to confirm or extend analysis
  2. Perform experiments yourself
84
Q

Define

Codon

A

a sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule

85
Q

Define

Template strand

A

the term that refers to the strand used by DNA polymerase or RNA polymerase to attach complementary bases during DNA replication or RNA transcription

86
Q

Definition

the collection, classification, storage, and analysis of biochemical and biological information using computers especially as applied in molecular genetics and genomics

A

Bioinformatics

87
Q

Define

Coding strand

A

The single strand of a separated double helix of DNA that has the same base sequence as the MESSENGER RNA (mRNA) formed from the complementary DNA strand

88
Q

Write the consensus seequence

A

T G A C G T C A T/A R N

Where R = purine, Y = pyrimidine, N = any

89
Q

Definition

a specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA

A

Methylguanosine cap

90
Q

Definition

a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance

A

Motif

91
Q

Definition

a virtual sequence which shows the most commonly found base at each particular position in a motif. In promotors, this can be thought of as the optimal sequence for binding RNA polymerase

A

Consensus sequence

92
Q

Definition

a mutation that exchanges one base for another (i.e., a change in a single “chemical letter” such as switching an A to a G)

A

Substitution

93
Q

Which of the following base-pairs is found in RNA?

Select one:

a. G:A
b. U:C
c. A:T
d. U:G

A

Which of the following base-pairs is found in RNA?

Select one:

a. G:A
b. U:C
c. A:T

d. U:G

94
Q

Prokaryotic mRNAs commonly contain…

Select one:

a. a polyadenylation signal
b. multiple ribosome binding sites
c. 5’ methyl guanosine caps
d. interrupted coding sequences

A

Prokaryotic mRNAs commonly contain…

Select one:

a. a polyadenylation signal

b. multiple ribosome binding sites

c. 5’ methyl guanosine caps
d. interrupted coding sequences

95
Q

Which type of RNA is not found in prokaryotes?

Select one:

a. messenger RNA
b. transfer RNA
c. small nucleolar RNA
d. untranslated RNA

A

Which type of RNA is not found in prokaryotes?

Select one:

a. messenger RNA
b. transfer RNA

c. small nucleolar RNA

d. untranslated RNA

96
Q

An open reading frame (ORF) is BEST described as a stretch of nucleotides…

Select one:

a. encoding a string of codons between termination codons
b. that is part of a coding sequence
c. that does not contain an intron
d. encoding a functional protein

A

An open reading frame (ORF) is BEST described as a stretch of nucleotides…

Select one:

a. encoding a string of codons between termination codons

b. that is part of a coding sequence
c. that does not contain an intron
d. encoding a functional protein

97
Q

Statistically, a stretch of sequence that has more than 60 uninterrupted codons has a less than ___% chance of occurring at random.

Select one:

a. 1%
b. 2%
c. 5%
d. 10%

A

Statistically, a stretch of sequence that has more than 60 uninterrupted codons has a less than ___% chance of occurring at random.

Select one:

a. 1%
b. 2%

c. 5%

d. 10%

98
Q

RNA has the ability to form stem and loop secondary structures. Which of the following is likely to be the most stable?

Select one:

a. 15 base pair stem; 1 base loop
b. 15 base pair stem; 10 base loop
c. 15 base pair stem; 7 base loop
d. 15 base pair stem; 4 base loop

A

RNA has the ability to form stem and loop secondary structures. Which of the following is likely to be the most stable?

Select one:

a. 15 base pair stem; 1 base loop
b. 15 base pair stem; 10 base loop

c. 15 base pair stem; 7 base loop

d. 15 base pair stem; 4 base loop

99
Q

The following diagram represents DNA containing a protein-encoding gene, and specifies the positions of its translational start and stop codons.

5 ‘ —————————CTA—/ / ——CAT——————- 3’

3 ‘ —————————GAT–/ / ——GTA——————-5’

The transcribed message (mRNA) will have the sequence:

Select one:

a. 3’ ————GAU–/ /——–GUA——5’
b. 5’————-CUA–/ /——–CAU——3’
c. 3’————-CUA–/ /——–CAU——5’
d. 5’ ————GAU–/ /——–GUA——3’

A

The following diagram represents DNA containing a protein-encoding gene, and specifies the positions of its translational start and stop codons.

5 ‘ —————————CTA—/ / ——CAT——————- 3’

3 ‘ —————————GAT–/ / ——GTA——————-5’

The transcribed message (mRNA) will have the sequence:

Select one:

a. 3’ ————GAU–/ /——–GUA——5’

b. 5’————-CUA–/ /——–CAU——3’
c. 3’————-CUA–/ /——–CAU——5’
d. 5’ ————GAU–/ /——–GUA——3’

100
Q

The “universal” genetic code describes how codons embedded in nucleic acids encode amino acids in proteins, and is used by all organisms (Fig 1). In 1979, researchers studying human mitochondrial genes reported that they use an alternative genetic code that differs slightly from the universal code (Fig 2). Subsequent work showed that mitochondria from other organisms also use slightly different codes.

How many synonymous codons for arginine are present in the universal code?

Select one:

a. 2
b. 6
c. 4
d. 1

A

How many synonymous codons for arginine are present in the universal code?

Select one:

a. 2

b. 6

c. 4
d. 1

101
Q

The “universal” genetic code describes how codons embedded in nucleic acids encode amino acids in proteins, and is used by all organisms (Fig 1). In 1979, researchers studying human mitochondrial genes reported that they use an alternative genetic code that differs slightly from the universal code (Fig 2). Subsequent work showed that mitochondria from other organisms also use slightly different codes.

How many termination codons are present in the mammalian mitochondrial code?

Select one:

a. 2
b. 4
c. 1
d. 6

A

How many termination codons are present in the mammalian mitochondrial code?

Select one:

a. 2

b. 4

c. 1
d. 6

102
Q

The “universal” genetic code describes how codons embedded in nucleic acids encode amino acids in proteins, and is used by all organisms (Fig 1). In 1979, researchers studying human mitochondrial genes reported that they use an alternative genetic code that differs slightly from the universal code (Fig 2). Subsequent work showed that mitochondria from other organisms also use slightly different codes.

How many codons are available in invertebrate mitochondrial DNA to encode serine?

Select one:

a. 6
b. 4
c. 2
d. 8

A

How many codons are available in invertebrate mitochondrial DNA to encode serine?

Select one:

a. 6
b. 4
c. 2

d. 8

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