BIOC0005 - MOLECULAR BIOLOGY; PLASMIDS; PCR;
OPERONS EXAM QUESTIONS AND ANSWERS WITH
COMPLETE VERIFIED SOLUTIONS
What is the centra dogma of molecular biology?
A model that explain the flow of genetic information within a cell.
Flow was originally considered to be unidirectional DNA → RNA → Protein.
Reverse transcription disproves this.
Can protein be the source of information flow?
No - only recipient, DNA and RNA can be both.
Who suggested the centra dogma?
Francis Crick (1956)
Briefly describe deoxyribonucleic acid.
Unbranched anionic polymer.
Composed of four different types of nucleotide.
Describe the four nucleotides.
Adenine and guanine are purines (base has 2 rings)
Cytosine and thymine are pyrimidines (base 1 ring)
Same 5-carbon deoxyribose sugar
Nucleotides linked by phosphodiester bonds between 5' and 3' carbons - condensation
reaction.
,What is the direction of DNA synthesis?
5' to 3'
How are the two DNA strands held together?
Weak H bonds between complementary base pairs of antiparallel chains.
A pairs with T (2H), C with G (3H)
Why does base-pair stacking occur in DNA?
Bases are hydrophobic, so it is energetically favorable for them to stack, held together
by π-π interactions. This causes the backbones to form a double-stranded helix.
Describe the most common structure of DNA.
Watson-Crick form (B-DNA)
A right-handed anti-parallel double helix.
~10.5 bp per 360 turn = rise of 3.32 nm (33.2 Å)
~2.0 nm (20 Å) in width
Possesses major and minor groves (important for protein interactions).
Right-handed means direction of fingers, anticlockwise
What are three forms of DNA other than B-DNA?
A-DNA - right-handed form when DNA is dehydrated
Z-DNA - left-handed double helix sometimes found naturally
Triple-helical DNA - A third strand can be incorporated into the B-form.
Describe an example of post-synthesis modification of DNA and its effects.
,Methylation of adenine or cytosine
Change the activity of a DNA segment without changing the sequence.
Mark a DNA strand as the parental strand during replication.
Methylation can result in 'open' euchromatin, whereas unmethylated DNA is 'closed'
heterochromatin
Describe the structure of RNA and its differences to DNA.
A non-branching polyanionic polymer of four different nucleotides.
3 differences: 5-carbon sugar moiety is ribose (extra OH group on the 2' carbon)
Thymine replaced by uracil (spontaneous deamination).
RNA molecules are single-stranded but can fold to form local double-stranded
secondary structures
RNA is shorter.
RNA came before DNA. Why was cytosine developed?
Stronger base pairing with guanine as uracil often bonds with alanine. If spontaneous
deamination occurs in DNA there are cellular processes to resolve this.
Why is there increased repulsion between complementary RNA strands?
Extra O- group on the ribose repels (stronger negative charge).
Can double-stranded RNA form?
Yes - dsRNA viruses or cell processes such as posttranscriptional gene silencing.
, Describe the location and functions of different classes of RNA molecules.
What roles require RNA secondary structure?
Ribosomal and transfer RNAs.
Describe the basic structure of proteins.
Unbranched polymer of L-amino acids joined by peptide bonds.
What is the direction of biological synthesis of proteins?
N to C terminus (processive and unidirectional)
Name the two extra proteinogenic amino acids.
Selenocysteine
Pyrrolysine
Explain the purpose of the genetic code.
Universal, defines the amino acids according to codons on the RNA strands.
(rare codon reassignments (usually involving UGA and UAG) are seen in some
prokaryotic and organelle genomes)
How are introns removed from RNA?
By splicing, which can give alternative outcomes.
Trans-splicing occurs between different gene products (called inteins and exteins.)
What is the maximum absorbance of DNA and RNA? What is this used for?
260 nm.
This is due to the ring structure of the bases.
To quantify DNA and RNA.
What does 1 A260 unit represent for dsDNA, ssDNA and ssRNA concentration?
OPERONS EXAM QUESTIONS AND ANSWERS WITH
COMPLETE VERIFIED SOLUTIONS
What is the centra dogma of molecular biology?
A model that explain the flow of genetic information within a cell.
Flow was originally considered to be unidirectional DNA → RNA → Protein.
Reverse transcription disproves this.
Can protein be the source of information flow?
No - only recipient, DNA and RNA can be both.
Who suggested the centra dogma?
Francis Crick (1956)
Briefly describe deoxyribonucleic acid.
Unbranched anionic polymer.
Composed of four different types of nucleotide.
Describe the four nucleotides.
Adenine and guanine are purines (base has 2 rings)
Cytosine and thymine are pyrimidines (base 1 ring)
Same 5-carbon deoxyribose sugar
Nucleotides linked by phosphodiester bonds between 5' and 3' carbons - condensation
reaction.
,What is the direction of DNA synthesis?
5' to 3'
How are the two DNA strands held together?
Weak H bonds between complementary base pairs of antiparallel chains.
A pairs with T (2H), C with G (3H)
Why does base-pair stacking occur in DNA?
Bases are hydrophobic, so it is energetically favorable for them to stack, held together
by π-π interactions. This causes the backbones to form a double-stranded helix.
Describe the most common structure of DNA.
Watson-Crick form (B-DNA)
A right-handed anti-parallel double helix.
~10.5 bp per 360 turn = rise of 3.32 nm (33.2 Å)
~2.0 nm (20 Å) in width
Possesses major and minor groves (important for protein interactions).
Right-handed means direction of fingers, anticlockwise
What are three forms of DNA other than B-DNA?
A-DNA - right-handed form when DNA is dehydrated
Z-DNA - left-handed double helix sometimes found naturally
Triple-helical DNA - A third strand can be incorporated into the B-form.
Describe an example of post-synthesis modification of DNA and its effects.
,Methylation of adenine or cytosine
Change the activity of a DNA segment without changing the sequence.
Mark a DNA strand as the parental strand during replication.
Methylation can result in 'open' euchromatin, whereas unmethylated DNA is 'closed'
heterochromatin
Describe the structure of RNA and its differences to DNA.
A non-branching polyanionic polymer of four different nucleotides.
3 differences: 5-carbon sugar moiety is ribose (extra OH group on the 2' carbon)
Thymine replaced by uracil (spontaneous deamination).
RNA molecules are single-stranded but can fold to form local double-stranded
secondary structures
RNA is shorter.
RNA came before DNA. Why was cytosine developed?
Stronger base pairing with guanine as uracil often bonds with alanine. If spontaneous
deamination occurs in DNA there are cellular processes to resolve this.
Why is there increased repulsion between complementary RNA strands?
Extra O- group on the ribose repels (stronger negative charge).
Can double-stranded RNA form?
Yes - dsRNA viruses or cell processes such as posttranscriptional gene silencing.
, Describe the location and functions of different classes of RNA molecules.
What roles require RNA secondary structure?
Ribosomal and transfer RNAs.
Describe the basic structure of proteins.
Unbranched polymer of L-amino acids joined by peptide bonds.
What is the direction of biological synthesis of proteins?
N to C terminus (processive and unidirectional)
Name the two extra proteinogenic amino acids.
Selenocysteine
Pyrrolysine
Explain the purpose of the genetic code.
Universal, defines the amino acids according to codons on the RNA strands.
(rare codon reassignments (usually involving UGA and UAG) are seen in some
prokaryotic and organelle genomes)
How are introns removed from RNA?
By splicing, which can give alternative outcomes.
Trans-splicing occurs between different gene products (called inteins and exteins.)
What is the maximum absorbance of DNA and RNA? What is this used for?
260 nm.
This is due to the ring structure of the bases.
To quantify DNA and RNA.
What does 1 A260 unit represent for dsDNA, ssDNA and ssRNA concentration?
