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DNA synthesis mind map
This is a synthetic mind map about DNA, including the basic laws of DNA replication, the enzymology and topology of DNA replication, etc.
Edited at 2023-11-14 21:08:02
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DNA synthesis mind map
- bacteria
This is a mind map about bacteria, and its main contents include: overview, morphology, types, structure, reproduction, distribution, application, and expansion. The summary is comprehensive and meticulous, suitable as review materials.
- Plant asexual reproduction
This is a mind map about plant asexual reproduction, and its main contents include: concept, spore reproduction, vegetative reproduction, tissue culture, and buds. The summary is comprehensive and meticulous, suitable as review materials.
- Reproductive development of animals
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- Outline
DNA synthesis
DNA synthesis in organisms or cells mainly includes processes such as DNA replication, DNA repair synthesis, and reverse transcription synthesis of DNA.
DNA replication is DNA synthesis using DNA as a template and is the process of genome replication.
Its essence is enzymatic deoxyribonucleotide polymerization reaction
The faithful replication of DNA is based on the rules of base pairing. Enzymatic repair system corrects possible errors in replication
The rules and processes of DNA replication in prokaryotes and eukaryotes are similar, but the DNA replication process in eukaryotes and the molecules involved are more complex and sophisticated.
Basic laws of DNA replication
DNA replication characteristics mainly include semi-conservative replication, double-sided replication and semi-discontinuous replication
DNA is replicated with high fidelity
DNA replicates in a semiconservative manner
The semi-conservative replication rule of DNA biosynthesis is one of the important discoveries in the mechanism of genetic information transmission.
The elucidation of the semi-conservative replication rule is of great significance to understanding the function of DNA and the continuity of species.
According to the semi-conservative replication method, all the genetic information of the parents is retained in the DNA of the offspring. The base sequences between the DNA of the parents and the offspring are highly consistent, which reflects the retention of inheritance.
Genetic conservatism is relative rather than absolute. The relative stability of genetic information is the molecular basis for species stability, but it does not mean that there are no differences between individuals of the same species.
There are three possibilities for the DNA template to remain in the progeny DNA, fully reserved, semi-reserved and mixed.
DNA replication proceeds in both directions from the origin
Cell proliferation depends on genome duplication so that offspring can obtain complete genetic information.
Prokaryotic genomes are circular DNA with only one origin of replication
The replication starts from the starting point and unwinds in both directions, and the bidirectional replication starts from a single point.
The replicating template DNA forms two open-stranded regions extending in opposite directions, called replication forks.
A replication fork refers to the Y-shaped region formed by replicating double-stranded DNA molecules.
A region of DNA replication starting from a DNA replication origin is called a replicon
A replicator is a functional unit that independently completes replication and contains an origin of replication.
Each chromosome has multiple origins, resulting in multi-origin bidirectional replication characteristics.
DNA replication occurs in a semi-discontinuous manner
One of the characteristics of the DNA double helix structure is that the two strands are antiparallel. One strand is in the 5' to 3' direction, and its complementary strand is in the 3' to 5' direction.
DNA polymerase can only catalyze the synthesis of DNA strands from the 5' to 3' direction, so when the daughter strand is copied along the template, it can only extend from the 5' to 3' direction.
during DNA replication
The synthesis of daughter strand DNA generated along the melting direction is continuous, and this strand is called the leading strand.
Because the replication direction is opposite to the unwinding direction, the other strand cannot be continuously extended. It can only generate primers from 5'→3' piece by piece as the template strand unwinds, and replicate the daughter strand. The template is opened for one section, and a sub-strand is synthesized at the beginning; another section is opened, and another sub-strand is synthesized at the beginning. This discontinuously copied strand becomes the lagging strand.
A new DNA fragment synthesized along the template strand of the lagging strand and named Okazaki fragment
DNA replication with high fidelity
DNA replication is highly fidelity
"Semi-conservative replication" ensures absolute guarantee of information transfer between parent and offspring DNA molecules
High-fidelity DNA polymerase utilizes strict base pairing principles as one of the mechanisms to ensure replication fidelity
Complex structure of replication forks in vivo provides replication accuracy
Enzymology and topology of DNA replication
DNA replication is an enzymatic nucleotide polymerization reaction
Substrate: dATP, dGTP, dCTP, dTTP
Polymerase: DNA-dependent DNA polymerase
Template: The mother strand of DNA is unwound into a single strand. Following the rules of base complementarity, the daughter strands are synthesized according to the guidance of the template. The daughter strands are extended in a direction.
Primer: Provides 3'-OH end with dNTP, which can be polymerized sequentially
DNA polymerase catalyzes the polymerization of deoxyribonucleotides
Characteristics of polymerase
DNA new strand generation RNA primers and templates
The new chain can only be extended in the 5' to 3' direction.
3' to 5' exonuclease activity: can identify mismatched base pairs and hydrolyze them
5' to 3' exonuclease activity: can excise mutated DNA fragments
Prokaryotes have at least five DNA polymerases
Mainly divided into three types
DNA polI, encoded by polA, mainly plays a role in DXA damage repair and plays an auxiliary role in semi-conservative replication.
DNA polII, encoded by polB, restarts replication forks when replication is blocked by damaged DYA
DNApolIII is encoded by polC. DNApolIII is the enzyme that actually catalyzes the replication and elongation of prokaryotes.
DNA pol III is an asymmetric heteropolymer composed of 10 subunits (17). It consists of 2 core enzymes connected to the y-complex, the clamp loading complex, through a sliding clamp composed of a pair of β subunits.
The core enzyme is composed of α, ε, and θ subunits. Its main function is to synthesize DNA and has 5' → 3' polymerization activity; the ε subunit is necessary for the fidelity of replication; the β subunit plays a role in clamping and stabilizing the DNA template strand, and The function of sliding the enzyme along the template; the remaining 7 subunits are collectively called the Υ-complex, including Υ, δ, δ, Ψ, χ and two T, which promote sliding clamp loading, assembly of the whole enzyme onto the template and strengthen the core The role of enzyme activity
The secondary structure of DNApolI is dominated by α-helices, and its main function is to proofread errors during replication and fill in gaps that occur during replication and repair.
Klenow fragment is a commonly used tool enzyme for laboratory synthesis of DNA and molecular biology research.
DNApolII has low template specificity. It can catalyze nucleotide polymerization even on damaged DNA templates. It is also involved in the emergency repair of DNA damage.
There are five common eukaryotic DNA polymerases
Base selection and proofreading functions of DNA polymerase
Three mechanisms to achieve fidelity
Follow strict base pairing rules
Base selection function of polymerase in replication elongation
There is a timely proofreading function when copying errors occur.
Replication fidelity relies on correct base selection
The key to DNA replication fidelity is correct base pairing, which in turn is the formation of hydrogen bonds
The dechained ribose sugar in DNA is connected to the base by a glycosidic bond. This piece has two conformations: cis and trans.
The exonuclease activity in the polymerase identifies and corrects mismatched bases during replication.
Exonuclease is an enzyme that can sequentially hydrolyze nucleic acid nucleotides from the end of the nucleic acid chain. Exonuclease is directional.
Prokaryotic DNA polI, eukaryotic DNA pol 8 and DNApols all have strong 3' → 5' exonuclease activity, which can identify and excise pre-matched bases during the replication process and correct replication errors. This process is also called mismatch repair
Topological changes in DNA molecules during replication
The bases of the DNA molecule are buried inside the double helix and can only function as a template if they are broken into single strands.
Multiple enzymes are involved in unwinding DNA and stabilizing the single-stranded state
The function of DNAB is to use ATP to unwind the double strands of DNA and act as a helicase.
Single-stranded binding proteins have the ability to bind single-stranded DNA, maintain the single-stranded stable state of the template, and protect it from degradation by nucleases that are widely present in cells.
Primase: an enzyme that catalyzes the production of RNA primers during the initiation of replication
DNA topoisomerase changes the supercoiled state of DNA
DNA topoisomerase, referred to as topozyme, is widely found in prokaryotes and eukaryotes. It is divided into type I and type II. Recently, topoisomerase III was discovered.
Topolases can both hydrolyze and connect phosphodiester bonds in DNA molecules.
Topoase I can cut one of the double strands of DNA so that the DNA will not get knotted during unwinding and rotation. When appropriate, it will seal the cut and make the DNA into a relaxed state. This reaction does not require ATP.
Topopase II can cut the double-stranded DNA in a positive supercoiled state at a certain position to relax the supercoil. Then, using ATP for energy, the broken ends of the relaxed DNA are connected and restored under the catalysis of the same enzyme.
DNA ligase ligates single-stranded gaps created during replication
Mode of action: Connects the 3'-OH end of a DNA chain to the 5'-P end of another DNA chain, forming a phosphodiester bond between the two, thus connecting two adjacent DNA chains into a complete chain.
Function
1DNA ligase not only plays the role of the final junction nick in replication
2 also plays a role in junction gaps in DNA repair and recombination.
3 is also one of the important tool enzymes for genetic engineering.
reverse transcription
Double-stranded DNA is the genetic material of most living things
The genetic material of some viruses is RNA
Plasmids of prokaryotes and mitochondrial DNA of eukaryotes are both extrachromosomal DNA.
These non-chromosomal genomes replicate in a special way
Retroviral genomic RNA replicates by reverse transcription mechanism
The genome of an RNA virus is RNA rather than DNA, and its replication method is reverse transcription, so it is also called a retrovirus.
The enzyme that catalyzes the synthesis of double-stranded DNA using RNA as a template is called reverse transcriptase
RNA viruses replicate into double-stranded DNA proviruses within cells
Proviruses retain all genetic information of RNA viruses and can reproduce independently within cells
The proviral genome is inserted into the cell genome through genetic recombination and is replicated and expressed along with the host genes. This type of reorganization is called integration
The discovery of reverse transcription developed the central dogma
The phenomenon of reverse transcription shows that at least in some organisms RNA also has the function of transmitting genetic information. This is a challenge to the traditional central dogma
The human immunodeficiency virus, the causative agent of AIDS, is also an RNA virus and has reverse transcription activity.
Molecular biology research also uses reverse transcriptase as one of the important methods to obtain target genes for genetic engineering. This method is called the cDNA method.
eukaryotic DNA replication process
Differences in DNA replication between eukaryotes and prokaryotes
1 Eukaryotes have many replicators, short Okazaki fragments, and slow replication fork advancement.
2DNA polymerase α/δ transition occurs from initiation to elongation phase of DNA replication
3. It is nuclease RNA that excises the Okazaki fragment RNA primer.
The initiation of DNA replication in eukaryotes is basically similar to that in prokaryotes
Eukaryotic DNA is distributed on many chromosomes, each chromosome has thousands of replicons, and there are many origins of replication
Replication is sequential, which means that the replicators are activated in groups rather than synchronously.
The core sequence (autonomous replication sequence) of yeast DNA replication origin is A(T)TTTATA(G)TTTA(T)
The initiation of replication requires the participation of DNA polα, polε, and polδ as well as helicase, topozyme and replication factors.
Proliferating cell nuclear antigen plays a key role in replication initiation and elongation
PCNA has the effect of promoting nucleosome production, and the protein level of PCNA is also an important indicator of cell proliferation ability.
Elongation of eukaryotic DNA replication occurs through DNA polymerase switching
DNApolα mainly catalyzes the synthesis of primers, and is quickly replaced by DNApolδ and DNApolε with continuous synthesis capabilities. This process is called polymerase switching. The former is mainly responsible for the trailing chain, and the latter is mainly responsible for the leading chain.
Eukaryotes replicate individually in replicon units, so the Okazaki fragments of primers and lagging strands are shorter than those of prokaryotes.
Eukaryotic DNA is assembled into nucleosomes immediately after synthesis
Two mechanisms for excision of primers
RNAseHI/FEN1-dependent excision method
DNA2/FEN1-dependent resection pattern
The number of nucleosome histone octamers is twice the length of one nucleosome DNA synthesized at the same time. Nuclear labeling experiments have proven that most of the original histones can be reassembled into the DNA chain, but in S phase cells also Large amounts and rapid synthesis of new histones
Telomerase is involved in solving the problem of chromosome end replication
Eukaryotic DNA replication and nucleosome assembly proceed simultaneously
Chromosomal DNA is a linear structure. The connection of Okazaki fragments during replication and the connection between replicons are easy to understand because they are all completed within the linear DNA.
A gap is left after the last replicated RNA primer on the DNA daughter strands at both ends of the chromosome is removed
Telomeres are the end structures of linear DNA molecules in eukaryotic chromosomes
significance:
1Maintain the stability of chromosomes
2 plays an important role in the integrity of DNA replication
3 cell division counter
4 length response telomerase activity
Telomerase consists of three parts: 451nt or 150~1300nt telomerase RNA, telomerase cooperating protein 1 and telomerase reverse transcriptase
significance:
1 Ensure complete replication of chromosome ends
2. Protective cap-like structures are formed at both ends of the chromosomes to protect the chromosomes from damage by enzymes and fusion of other chromosome ends.
3 plays an important role in cell lifespan, aging and death, as well as the occurrence and treatment of tumors
Telomerase activity is not necessarily proportional to telomere length
Eukaryotic chromosomal DNA can only be replicated once per cell cycle
An important feature of eukaryotic chromosomal DNA replication is that replication only occurs during the S phase of the cell cycle and can only be replicated once.
The initiation of DNA replication in eukaryotic cells occurs in two steps
Selection of replicator genes
Replicators refer to all DNA sequences necessary for the initiation of DNA replication.
This selection occurs during the G1 phase, during which prereplication complexes are assembled at each replicating locus in the genome.
Activation of replication origin
Appearing only after cells enter S phase, this phase will activate pre–RC, recruit several replication gene binding proteins and DNA polymerase, and initiate DNA unwinding.
Activation of replication origins coincides with cell cycle progression
Replication permission factors are CDK substrates and are required to initiate DNA replication.
Eukaryotic mitochondrial DNA replicates in a D-loop manner
D-loop replication is how mitochondrial DNA is replicated
The characteristic of base loop replication is that the origin of replication is not at the same site on the double-stranded DNA. There are sequential differences in the replication of the inner and outer loops.
prokaryotic DNA replication process
start of replication
Initiation is a relatively complex step in replication. During this process, various enzymes and protein factors assemble primers at the origin of replication to form replication forks and synthesize RNA primers.
unzipping of DNA
Copy has a fixed starting point
Origin of replication: oriC
This DNA has five sets of tandem repeats consisting of 9 base pairs, forming the DNA A binding site and three sets of AT-rich regions consisting of 13 base pairs of tandem repeats.
The pairing between ATs in the DNA double strand is maintained by only two hydrogen bonds, so the AT-rich parts are prone to melting.
DNA unzipping requires the participation of multiple proteins
The unzipping process of DNA is completed by three proteins: DNA, DNA B, and DNA C.
The DNA protein is a homotetramer that is responsible for recognizing and binding to the tandem repeats of oriC.
DNA topoisomerase is required for the unzipping process
Unchaining is a high-speed reverse rotation and knotting is bound to occur downstream.
Negatively supercoiled DNA acts as a better template than positively supercoiled DNA
Primer synthesis and initiation complex formation
The replication initiation process requires the first synthesis of primers, which are short-chain RNA molecules catalyzed by primase (the enzyme that catalyzes the synthesis of RNA primers at the initiation of replication).
At this time, an initiation complex structure containing helicase DNA B, DNA C, primase and the replication initiation region of DNA is formed. This structure is also called a initiator in the phage φχ system.
Movement of the protein components of the initiation complex along the DNA chain requires energy supplied by ATP
DNA chain elongation
The elongation of the DNA chain during replication is catalyzed by DNA pol. The enzyme that catalyzes the elongation reaction in prokaryotes is DNApolIII.
Its chemical essence is the continuous formation of phosphodiester bonds
Replication extends along the 5' to 3' direction, which refers to the direction of daughter strand synthesis. The leading strand extends continuously along the 5' to 3' direction, while the trailing strand extends discontinuously along the 5' to 3' direction.
On the same replication fork, the leading strand replicates before the lagging strand, but both sides are elongated under the catalysis of the same DNApolIII.
The direction of melting is the direction in which the enzyme is going and the direction in which the replication fork stretches forward.
Termination of replication
The termination process of replication includes excision of primers, filling of gaps and continuous incisions
The completion of replication also includes removing the RNA primer and replacing it with DNA, and finally contiguous DNA fragments into complete daughter strands