The Central Dogma of Molecular Biology Flashcards
How does mRNA ensure that genetic information is used effeciently?
- Only necessary genes are active
- The amount of gene product is easily controlled and can vary from gene to gene
- Distinct proteins can be synthesised from a single gene via mRNA modification (splicing)
An _________________ is defined as a DNA or RNA sequence which contains a run of codons uninterupted by a stop codon
An open reading frame (ORF) is defined as a DNA or RNA sequence which contains a run of codons uninterupted by a stop codon
Definition
the loss or gain of a nucleotide causing a shift in the reading frame
Deletion/Insertion
What is the optimum loop size of an RNA?
7 bases
RNA is synthesised in a __ to __ direction
RNA is synthesised in a 5’ to 3’ direction
i.e. is is added at the 3’ end
Define
Central Dogma
the two-step process, transcription and translation, by which the information in genes flows into proteins: DNA → RNA → protein.
Define
miRNA
a small non-coding RNA molecule
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)
Open reading frame (ORF)
Give an example of a positively charged R group
Single-stranded RNA can form intra-molecular base-pairs between ______________ to form antiparallel double stranded structures or _________
Single-stranded RNA can form intra-molecular base-pairs between inverted repeats to form antiparallel double stranded structures or stem-loops
Definition
A codon that signals the first amino acid to be used in the synthesis of the polypeptide chain of a protein
Initiation codon
A stretch of DNA that encodes a protein is called what?
Coding sequence
Define
Shine-Dalgano sequence
a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG
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
Template strand
Definition
an enzyme that is responsible for copying a DNA sequence into an RNA sequence, during the process of transcription
RNA polymerase
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
Coding strand
The initiation sequence of a prokaryotic mRNA is preceeded by what?
Ribosome binding site (Shine-Dalgano sequence)
Definition
relating to or denoting organic compounds in which carbon atoms form open chains (as in the alkanes), not aromatic rings
Aliphatic
RNA is produced using which strand of DNA?
Template strand
Definition
either of two sections, one on each side of a coding sequence on a strand of mRNA
Untranslated regions (UTR)
Define
Substitution
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)
What are the termination codons?
TAA, TAG, TGA
What processes is RNA structure crucial for?
- Transcription, in termination, splicing and transport
- Regulation of RNA stability
- Translation, in initiation, elongation, termination and regulation
- Catalysis
How are the untranslated regions of mRNA important?
Untranslated regions provide binding sites for proteins that stabilise, destabilise or transport RNA
What is a tRNA with an attached amino acid called?
Aminoacyl or “charged” tRNA
What motifs can signal whether an ORF is part of a real protein coding sequence?
- Promotor
- Ribosome binding site
Define
Methylguanosine cap
a specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA
What is the key to identifying the most likely structure of an RNA?
Thermodynamics - the more energy that is released, the more stable the structure (-ve ΔG = stable)
Definition
a small non-coding RNA molecule
miRNA
Define
Aliphatic
relating to or denoting organic compounds in which carbon atoms form open chains (as in the alkanes), not aromatic rings
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
Anticodon
Define
Polyadenylation
the addition of a poly(A) tail to a messenger RNA
True or False:
RNA can base pair with DNA or RNA
True
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.
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.
Define
Open reading frame (ORF)
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)
Give an example of a nonpolar, aliphatic R group
What types of RNA are produced in both prokaryotes and eukaryotes?
mRNA
rRNA
tRNA
antisense RNA
Definition
a sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule
Codon
Define
Motif
a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance
What is the initiation codon?
ATG - methionine (Met)
Give an example of a polar, uncharged R group
Define
Gene splicing
a post-transcriptional modification in which a single gene can code for multiple proteins
Definition
a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG
Shine-Dalgano sequence
Define
Promotor sequence
DNA sequences that define where transcription of a gene by RNA polymerase begins
How are the ends of the mRNA modified in eukaryotes?
A 7-methylguanosune “cap” is added to the 5’ end
A “tail” of A is added to the 3’ end
True or False:
All coding sequences are ORFs but not all ORFs are coding sequences
Define
Untranslated regions (UTR)
either of two sections, one on each side of a coding sequence on a strand of mRNA
Definition
the nucleic acid blueprint for a protein
Coding sequence
Which bases pair together in RNA?
A pairs with U
G pairs with C
G pairs with U
What is the minimum amount of amino acids encoded by a ORF needed for you to conclude that it is part of a gene?
60 amino acids
How many total reading frames are there in double stranded DNA?
6 (3 per strand)
Give an example of an aromatic R group
Define
Deletion/Insertion
the loss or gain of a nucleotide causing a shift in the reading frame
In transcription, the template is always read in direction __ to __
In transcription, the template is always read in direction 3’ to 5’
The function of tRNAs depends on sequence and ________ structure
The function of tRNAs depends on sequence and tertiary structure
Define
Consensus sequence
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
Define
Termination codon
a nucleotide triplet within messenger RNA that signals a termination of translation into proteins
Define
Initiation codon
A codon that signals the first amino acid to be used in the synthesis of the polypeptide chain of a protein
Definition
DNA sequences that define where transcription of a gene by RNA polymerase begins
Promotor sequence
Why is prokaryotic mRNA very unstable?
There is no modifications made to the 5’ and 3’ ends like in eukaryotes
Define
Anticodon
a sequence of three nucleotides forming a unit of genetic code in a transfer RNA molecule, corresponding to a complementary codon in messenger RNA
By convention, how is an RNA sequence written?
Written as texxt in the 5’ to 3’ direction, from left to right
What are coding sequences made up of?
Open reading frames (ORFs) that contain a start codon and are flanked by regulatory motifs which direct production of RNA
Definition
the addition of a poly(A) tail to a messenger RNA
Polyadenylation
Definition
the two-step process, transcription and translation, by which the information in genes flows into proteins: DNA → RNA → protein.
Central Dogma
True or False:
An ORF must (almost always) start with a Met, but a coding sequence may start with any anino acid
False
A coding sequence must (almost always) start with a Met, but an ORF may start with any anino acid
RNA is an exact copy of which of the strands of DNA?
Coding strand
Define
Reading frame
a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets
What are the differences between prokaryotic and eukaryotic mRNAs?
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
True or False:
tRNA has the codon
False
tRNA has the anticodon; mRNA has the codon
What can repeats in DNA indicate?
- Binding sites for proteins
- The presence of mobile genetic elements
- Contribute to single-stranded nucleic acid secondary structure
Define
Bioinformatics
the collection, classification, storage, and analysis of biochemical and biological information using computers especially as applied in molecular genetics and genomics
Give an example of a negatively charged R group
Definition
a post-transcriptional modification in which a single gene can code for multiple proteins
Gene splicing
Define
Coding sequence
the nucleic acid blueprint for a protein
Definition
a nucleotide triplet within messenger RNA that signals a termination of translation into proteins
Termination codon
What types of RNA are produced in only eukaryotes?
microRNA
snRNA
snoRNA
siRNA
True or False:
Base pairing in RNA is the same as DNA
False
G can also weakly pair with U
Define
RNA polymerase
an enzyme that is responsible for copying a DNA sequence into an RNA sequence, during the process of transcription
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
Reading frame
What are the steps of annotated a DNA sequence?
- Analyse sequence and add information on:
- Transcripts encoded
- Proteins encoded
- Binding sites for machinery
- Evolution
- Research scientific literature for experimental data to confirm or extend analysis
- Perform experiments yourself
Define
Codon
a sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule
Define
Template strand
the term that refers to the strand used by DNA polymerase or RNA polymerase to attach complementary bases during DNA replication or RNA transcription
Definition
the collection, classification, storage, and analysis of biochemical and biological information using computers especially as applied in molecular genetics and genomics
Bioinformatics
Define
Coding strand
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
Write the consensus seequence
T G A C G T C A T/A R N
Where R = purine, Y = pyrimidine, N = any
Definition
a specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA
Methylguanosine cap
Definition
a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance
Motif
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
Consensus sequence
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)
Substitution
Which of the following base-pairs is found in RNA?
Select one:
a. G:A
b. U:C
c. A:T
d. U:G
Which of the following base-pairs is found in RNA?
Select one:
a. G:A
b. U:C
c. A:T
d. U:G
Prokaryotic mRNAs commonly contain…
Select one:
a. a polyadenylation signal
b. multiple ribosome binding sites
c. 5’ methyl guanosine caps
d. interrupted coding sequences
Prokaryotic mRNAs commonly contain…
Select one:
a. a polyadenylation signal
b. multiple ribosome binding sites
c. 5’ methyl guanosine caps
d. interrupted coding sequences
Which type of RNA is not found in prokaryotes?
Select one:
a. messenger RNA
b. transfer RNA
c. small nucleolar RNA
d. untranslated RNA
Which type of RNA is not found in prokaryotes?
Select one:
a. messenger RNA
b. transfer RNA
c. small nucleolar RNA
d. untranslated RNA
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
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
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%
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%
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
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
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’
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’
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
How many synonymous codons for arginine are present in the universal code?
Select one:
a. 2
b. 6
c. 4
d. 1
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
How many termination codons are present in the mammalian mitochondrial code?
Select one:
a. 2
b. 4
c. 1
d. 6
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
How many codons are available in invertebrate mitochondrial DNA to encode serine?
Select one:
a. 6
b. 4
c. 2
d. 8
