Structural Aspects of DNA relevant to use in PCR Genetic material consists of a double stranded DNA with a sequence of 4 bases which determines the genetic code including Adenine (A), Guanine (G), Thumine (T) and Cytosine (C). These are all found on a deoxyribose backbone with bases linked to opposite strand by hydrogen bonds.
In the prokaryotic genome the DNA is a single circle, packaged by DNA binding proteins. DNA forms loops or domains (50-100) constrained by a protein core attached to the cell wall. Bacterial DNA is further compacted by twisting the DNA in each domain around itself called supercoiling, bacterial DNA is negatively supercoiled.
Supercoiling is controlled by a group of enzymes called topoisomerases. During replication, the unwinding of DNA may cause the formation of tangling structures, such as supercoils catenanes. The major role f the topoisomerase to prevent the DNA from tangling. Topoisomerase I causes relaxation of the supercoil while topoisomerase II (DNA gyrase) induces negative supercoils in newly replicated DNA.
Replication, Transcription and Translation. Replication Fidelity Some DNA polymerases have proof reading ability as in they can detect mistakes in nucleotide pairing. If a mistake is detected, polymerisation stops and it uses a 3’ to 5’ exonuclease activity to remove the incorrect nucleotide and allows another attempt. DNA polymerase proof reading ability varies and affects rates of spontaneous mutation.
Protein Synthesis Expression of genes occurs predominantly through production of proteins. Conversion of nucleic acid (DNA) info to proteins involves transcription and translation. Transcription is the conversion of DNA information into messenger RNA (mRNA). RNA differs from DNA in structure of bond between bases and the use of uracile rather than Thymine, RNA is also typically single stranded. Translation is the conversion of RNA information into a chain of amino acids.
Transcription The process of transcription is carried out by RNA polymerase. The newly synthesised mRNA reflects the template DNA strand. Only one strand of DNA is transcribed, which strand varies between specific regions. mRNA is comparatively short molecules (often just a few kilobases) and a large number of signals around chromosomes which regulate where transcription starts and stops. The start signals are called promoters which convey info on which direction and which strand to transcribe. The one DNA strand can be the template for multiple RNA polymerases to make multiple copies of mRNA’s at once.
Transcription Termination – Bacteria Terminator sequence is the one responsible for stopping transcription at the end of a gene. The characteristic feature is the presence of an inverted repeat- a short sequence that is complimentary to and in reverse direction from a region just preceding it. Often the termination sequence has a stem and loop structure often followed by a run of U (Uracil) residues.
Operons Cistron is a region of DNA coding for a specific polypptide chain (single protein). An operon are bacterial genes with related functions located together in a group (AKA a group of cistrons or a single promoter site, transcribed into a single polycistronic mRNA molecule carrying the information for several proteins-related proteins can be manufactured at the same time). Eukaryotic mRNA is generally monocistronic.
Translation Translation consists of three stages, Initiation, elongation and termination. During initiation, ribosomes (rRNA) attach to mRNA. During elongation, there is movement of the ribosomes along the mRNA strand reading it in codones (triplets of mRNA bases). Recognition of codon occurs by transfer RNA (tRNA) and binding. Attachment of amino acid bound to tRNA to string of amino acids (polypeptide chain). In Termination the reading of the mRNA sequence is terminated releasing the rRNA and polypeptide chain.
Reading Frame mRNA is read in consecutive groups of 3 bases. It could code for 3 different proteins depending on where it starts, ie, there are 3 potential reading frames. However, protein synthesis starts at a specific triplet (usually AUG, an initiation codon). The position of the ribosome binding site and the initiation codon determines the reading frame.
Post-translational modification After being translated, the protein has to fold correctly which is complicated and difficult to predict. Multiple polypeptide chains often associate to form a complete protein (such as rRNA). Sections of proteins may be cleaved to produce the mature protein (such as secretion proteins). Proteins may also have non-protein components added (such as glycoproteins).
Learn More
Crash course Biology: DNA Structure and Replication
Protein Post Translational Modification
Bleier Biology: Prokaryotic vs Eukaryotic Genomes
Questions
In the prokaryotic genome the DNA is a single circle, packaged by DNA binding proteins. DNA forms loops or domains (50-100) constrained by a protein core attached to the cell wall. Bacterial DNA is further compacted by twisting the DNA in each domain around itself called supercoiling, bacterial DNA is negatively supercoiled.
Supercoiling is controlled by a group of enzymes called topoisomerases. During replication, the unwinding of DNA may cause the formation of tangling structures, such as supercoils catenanes. The major role f the topoisomerase to prevent the DNA from tangling. Topoisomerase I causes relaxation of the supercoil while topoisomerase II (DNA gyrase) induces negative supercoils in newly replicated DNA.
Replication, Transcription and Translation. Replication Fidelity Some DNA polymerases have proof reading ability as in they can detect mistakes in nucleotide pairing. If a mistake is detected, polymerisation stops and it uses a 3’ to 5’ exonuclease activity to remove the incorrect nucleotide and allows another attempt. DNA polymerase proof reading ability varies and affects rates of spontaneous mutation.
Protein Synthesis Expression of genes occurs predominantly through production of proteins. Conversion of nucleic acid (DNA) info to proteins involves transcription and translation. Transcription is the conversion of DNA information into messenger RNA (mRNA). RNA differs from DNA in structure of bond between bases and the use of uracile rather than Thymine, RNA is also typically single stranded. Translation is the conversion of RNA information into a chain of amino acids.
Transcription The process of transcription is carried out by RNA polymerase. The newly synthesised mRNA reflects the template DNA strand. Only one strand of DNA is transcribed, which strand varies between specific regions. mRNA is comparatively short molecules (often just a few kilobases) and a large number of signals around chromosomes which regulate where transcription starts and stops. The start signals are called promoters which convey info on which direction and which strand to transcribe. The one DNA strand can be the template for multiple RNA polymerases to make multiple copies of mRNA’s at once.
Transcription Termination – Bacteria Terminator sequence is the one responsible for stopping transcription at the end of a gene. The characteristic feature is the presence of an inverted repeat- a short sequence that is complimentary to and in reverse direction from a region just preceding it. Often the termination sequence has a stem and loop structure often followed by a run of U (Uracil) residues.
Operons Cistron is a region of DNA coding for a specific polypptide chain (single protein). An operon are bacterial genes with related functions located together in a group (AKA a group of cistrons or a single promoter site, transcribed into a single polycistronic mRNA molecule carrying the information for several proteins-related proteins can be manufactured at the same time). Eukaryotic mRNA is generally monocistronic.
Translation Translation consists of three stages, Initiation, elongation and termination. During initiation, ribosomes (rRNA) attach to mRNA. During elongation, there is movement of the ribosomes along the mRNA strand reading it in codones (triplets of mRNA bases). Recognition of codon occurs by transfer RNA (tRNA) and binding. Attachment of amino acid bound to tRNA to string of amino acids (polypeptide chain). In Termination the reading of the mRNA sequence is terminated releasing the rRNA and polypeptide chain.
Reading Frame mRNA is read in consecutive groups of 3 bases. It could code for 3 different proteins depending on where it starts, ie, there are 3 potential reading frames. However, protein synthesis starts at a specific triplet (usually AUG, an initiation codon). The position of the ribosome binding site and the initiation codon determines the reading frame.
Post-translational modification After being translated, the protein has to fold correctly which is complicated and difficult to predict. Multiple polypeptide chains often associate to form a complete protein (such as rRNA). Sections of proteins may be cleaved to produce the mature protein (such as secretion proteins). Proteins may also have non-protein components added (such as glycoproteins).
Learn More
Crash course Biology: DNA Structure and Replication
Protein Post Translational Modification
Bleier Biology: Prokaryotic vs Eukaryotic Genomes
Questions
- The enzyme that catalyzes the synthesis of DNA is called?
- What links together the nitrogenous bases in the center of the DNA molecule?
- What is the role of DNA polymerase?
- Why can't DNA polymerase work continuously on both parent strands?