DNA & Genomics Flashcards
ATCG Ratio
Ratios of A:T and C:G are approximately 1:1, indicating complementary base pairing where A pairs with T and C pairs with G. Multiple hydrogen bonds formed between complementary nitrogenous base pairs help to stabilise the structure of DNA.
Pairing of purine and pyrimidine bases ensures constant width of DNA double helix.
DNA molecule
1) Box up a nucleotide
2) Deoxyribose sugar is pentagon with O at top
3) Phosphate groups are attached to C3 and C4
4) Phosphodiester bonds point to both and label.
5) Draw and label hydrogen bonds between nitrogenous bases
6) Label 5’ and 3’
Proof of semi-conservative replication
Parental DNA molecule is split into two strands and each strand is used as template for synthesis of complementary, genetically identical daughter strands by addition of free nucleotides by complementary base pairing. Results in production of hybrid daughter DNA molecules with one parental strand and one daughter strand
Anti-parallel
One strand is synthesised continuously from 5’ to 3’, known as leading strand, while other strand which runs in opposite direction 3’ to 5’ is synthesised discontinuously since DNA polymerase only synthesises from 5’ to 3’ with their DNA polymerases extending new strands in opposite direction of replication fork.
DNA molecule has two sugar phosphate backbones and are aligned parallel to each other but pointing in opposite directions.
Replication
Helicase binds to the origin replication and unzips the double helix of DNA by breaking hydrogen bonds to form a replication fork. Single-stranded DNA binding proteins prevent the two strands from reannealing. Topoimerase relieves unwinding strain by swivelling, breaking and rejoining DNA ahead of the replication fork.
DNA Polymerase III synthesises complementary daughter strand from 5’ to 3’ direction by adding free deoxyribonucleotides which complementary base pair to the template parental strand, where A forms 2 H bonds with T and C forms 3 with G. It then catalyses formation of phosphodiester bonds between nucleotides.
(Part of enzyme also proofreads the previous region to ensure correct base pairing by replacing incorrect nucleotides with correct ones, ensuring fidelity of DNA sequence)
On the leading strand, synthesis of daughter strand is continuous while on the anti-parallel lagging strand which is 3’ to 5’, synthesis is discontinuous. Primase synthesises RNA primers which provides 3’OH ends for DNA Polymerase III to add nucleotides to. After that, the RNA primers are excised by DNA Polymerase I and DNA is synthesised in its place. The resulting DNA ligase seals the nicks between Okazaki fragments by catalysing formation of phosphodiester bonds between fragments to form the second continuous daughter strand.
Replication of lagging strand
Long version:
Since the two strands of DNA are anti-parallel, one strand is synthesised continuously from 5’ to 3’ while the strand which is 3’ to 5’ is synthesised discontinuously because DNA polymerase only works from 5’ to 3’ with DNA polymerases extending strands in opposite directions to replication fork.
Hence, primase catalyses synthesis of RNA primers which provide 3’OH end for DNA Polymerase III to add free nucleotides to by complementary base pairing and catalyse formation of phosphodiester bonds between nucleotides. DNA Polymerase I then excises the RNA primers and replaces them with DNA, leading to formation of Okazaki fragments. DNA ligase seals the nicks between fragments by catalysing formation of phosphodiester bonds between nucleotides.
Role of mRNA
mRNA acts as a medium of information that allows for polypeptides to be produced from the genes coding for them.
Role of rRNA
rRNA associates with a set of ribosomal proteins to form small ribosomal subunits and large ribosomal subunits.
In the small ribosomal subunit, specific rRNA sequence allow ribosomes to bind to start codon on mRNA by complementary base pairing to begin translation. In the large ribosomal subunit, rRNA allows aminoacyl transfer RNA to enter aminoacyl site and peptidyl site. Also contains peptidyl transferase which catalyses formation of peptide bonds between amino acids to form polypeptide.
Role of tRNA
Each tRNA contains specific anticodon that is matched to a specific amino acid, joined by aminoacyl-tRNA synthetase.
When aminoacyl-tRNA enters the ribosome, anticodon complementary base pairs with codon on mRNA, allowing for specific sequence of nucleotides on mRNA to be translated accurately to specific sequence of amino acids to form polypeptide.
When peptide bond is formed between its amino acid and the previous, tRNA is released and reused by being attached to another specific amino acid.
Replication vs Transcription
1) Replication produces double-stranded DNA while transcription produces a single-stranded messenger RNA.
2) Replication involves DNA polymerase that synthesises a complementary DNA strand while transcription involves RNA polymerase which synthesises a complementary RNA strand.
3) In replication, both strands are used as templates while in transcription only one strand is used as a template.
4) Replication occurs only in synthesis phase while transcription takes place constantly except for during nuclear division.
5) Replication requires RNA primers to initiate while transcription does not.
Both take place in the nucleus.
Both are carried out by enzymes called polymerases
Both require DNA as a template and free nucleotides are added by complementary base pairing
Both involve catalysis of pdiester bonds
Transcription vs Translation
1) Transcription occurs in the nucleus, translation occurs in ribosomes in the cytosol or on RER.
2) Transcription involves RNA polymerase to synthesise complementary mRNA strand, translation involves ribosomes and tRNA to synthesise polypeptide.
3) Transcription involves catalysis of phosphodiester bonds between ribonucleotides, translation involves catalysis of peptide bonds between amino acids.
4) Transcription uses DNA as a template to synthesise mRNA, translation uses mRNA as a template to synthesise polypeptide.
5) Linked by RNA polymerase vs linked by peptidyl transferase
6) In transcription, DNA template is read from 3’ to 5’ while mRNA is read 5’ to 3’.
Both take place constantly except for during nuclear division.
Both involve complementary base pairing??
Transcription
RNA Polymerase and GTFs bind to the promoter region, assembling the transcription initiation complex. RNA Polymerase unzips and separates the two strands. RNA Polymerase translocates in 3’ to 5’ direction with respect to DNA strand, synthesising mRNA in 5’ to 3’ by adding free nucleotides by complementary base pairing and then catalysing phosphodiester bond formation between nucleotides.
Genetic Code
Made up of triplet codons each with three consecutive nucleotide bases
1) Universal, same sequence of nucleotides code for the same amino acid in all living organisms.
2) Degenerate, one amino acid may be coded for by more than one triplet codon.
3) Unambiguous, every codon corresponds to only one amino acid.
4) Non-overlapping, is read as 3 successive nucleotides. No nucleotides are skipped and the code is continuous.
Proof of semi-conservative replication
Parental DNA molecule is split into two strands and each strand is used as template for synthesis of complementary, genetically identical daughter strands by addition of free nucleotides by complementary base pairing. Results in production of hybrid daughter DNA molecules with one parental strand and one daughter strand
Anti-parallel
One strand is synthesised continuously from 5’ to 3’, known as leading strand, while other strand which runs in opposite direction 3’ to 5’ is synthesised discontinuously since DNA polymerase only synthesises from 5’ to 3’ with their DNA polymerases extending new strands in opposite direction of replication fork.
DNA molecule has two sugar phosphate backbones and are aligned parallel to each other but pointing in opposite directions.
Replication
Helicase binds to the origin replication and unzips the double helix of DNA by breaking hydrogen bonds to form a replication fork. Single-stranded DNA binding proteins prevent the two strands from reannealing. Topoimerase relieves unwinding strain by swivelling, breaking and rejoining DNA ahead of the replication fork.
DNA Polymerase III synthesises complementary daughter strand from 5’ to 3’ direction by adding free deoxyribonucleotides which complementary base pair to the template parental strand, where A forms 2 H bonds with T and C forms 3 with G. It then catalyses formation of phosphodiester bonds between nucleotides.
(Part of enzyme also proofreads the previous region to ensure correct base pairing by replacing incorrect nucleotides with correct ones, ensuring fidelity of DNA sequence)
On the leading strand, synthesis of daughter strand is continuous while on the anti-parallel lagging strand which is 3’ to 5’, synthesis is discontinuous. Primase synthesises RNA primers which provides 3’OH ends for DNA Polymerase III to add nucleotides to. After that, the RNA primers are excised by DNA Polymerase I and DNA is synthesised in its place. The resulting DNA ligase seals the nicks between Okazaki fragments by catalysing formation of phosphodiester bonds between fragments to form the second continuous daughter strand.
Replication of lagging strand
Long version:
Since the two strands of DNA are anti-parallel, one strand is synthesised continuously from 5’ to 3’ while the strand which is 3’ to 5’ is synthesised discontinuously because DNA polymerase only works from 5’ to 3’ with DNA polymerases extending strands in opposite directions to replication fork.
Hence, primase catalyses synthesis of RNA primers which provide 3’OH end for DNA Polymerase III to add free nucleotides to by complementary base pairing and catalyse formation of phosphodiester bonds between nucleotides. DNA Polymerase I then excises the RNA primers and replaces them with DNA, leading to formation of Okazaki fragments. DNA ligase seals the nicks between fragments by catalysing formation of phosphodiester bonds between nucleotides.
Role of mRNA
mRNA acts as a medium of information that allows for polypeptides to be produced from the genes coding for them.
