Notes for Biology
1.Order of Magnitudes
Speed
| Process | Speed |
|---|---|
| DNA Replication | bacteria: 1000 nuleotides/second eukaryotes: 50 nuleotides/second |
| each RNA polymerase | 50 nuleotides/second |
| Dividing of E.coli | once/30 minutes |
Length
| Strip | Length |
|---|---|
| Leading Strand | \(\infty\) |
| Lagging Strand | 1000~2000 nuleotides for bacteria 100~200 nuleotitdes for eukaryotes |
| RNA primers | 10 nuleotides for eukaryotes |
| Intervals between RNA primers on lagging strand | 100~200 nuleotides |
| RPA (domains of SSB) covers | 8 nuleotides |
| genome of E. coli | \(4.6\times10^6\) nucleotide pairs |
| average-size human chromosome | \(150\times10^6\) nucleotides |
| mitochondrion | length: \(1\sim2\mu \mathrm{m}\) width: \(0.1\sim 0.5 \mu \mathrm{m}\) |
Rate
| Process | Rate |
|---|---|
| DNA Replication | error rate: \(\frac{1}{10^{10}}\) |
| DNA Bases Tautomer | \(\frac{1}{10^{4}}\)~\(\frac{1}{10^{5}}\) |
| 5’\(\rightarrow\) 3’ polymerization(DNA) | error rate: \(\frac{1}{10^5}\) |
| 3’\(\rightarrow\) 5’ exonucleolytic proofreading(DNA) | error rate: \(\frac{1}{10^2}\) |
| strand-directed mismatch repair(DNA) | error rate: \(\frac{1}{10^3}\) |
| RNA polymerase | error rate: \(\frac{1}{10^4}\) |
Ratio
| Subatances | Ratio |
|---|---|
| ATP : dATP | 500 : 1 |
| mRNA : RNA | 3~5 : 100 |
Number
| Object | Number |
|---|---|
| replication origin | bacteria: 1 eukaryote: 30,000~50,000 |
| unicellular bacterium | 500 genes |
| a human | 25,000 genes |
| types of mRNA in each cell | 10~15 |
Duration
| Process | Duration |
|---|---|
| DNA Synthesis phase S phase | mammalian cell: 8 hours yeast: 40 minutes |
2.Protein and its Function
DNA Replication
| Protein | Function |
|---|---|
| DNA polymerase | 1.free deoxyribonuleoside triphosphates \(\rightarrow\) DNA 2.proof reading |
| 3’-to-5’ proof reading exonuclease (a subunit or protein domain of DNA polymerase) | self-correcting |
| Polymerase ε | synthesize leading strand in eukaryotes |
| Polymerase α Polymerase δ | synthesize lagging strand in eukaryotes Polα: RNA primer+ 20 n.t.; Polδ: 200n.t.; mismatch repair |
| DNA primase | free ribonuleoside triphosphates \(\rightarrow\) RNA primers on the lagging strand |
| DNA ligase | joins the 3’ and 5’ ends of DNA |
| DNA helicase | 5’ to 3’ along template strand in bacteria |
| DNA-binding proteins (Single Strand+…, SSB) | prevent hairpin formation |
| RPA(Replication Protein A): two DNA binding domains of SSB | |
| Sliding Clamp | holds DNA polymerase onto DNA |
| Clamp loader | load clamp onto DNA |
| DNA topoisomerase: a reversible nulease | type I: single strand break type II: double strand break |
| Initiator protein | |
| Helicase loading protein | |
| ORC | origin recognition complex |
DNA Transcription
| Protein | Function |
|---|---|
| RNA polymerase | 1.unwinding DNA helix 2.free ribonuleoside triphosphates \(\rightarrow\) RNA |
Homologous Recombination (HR)
| Protein | Function |
|---|---|
| RecA | E. coli Homologous recombination searching and strand exchange |
| Rad51 | eukaryotes Homologous recombination searching and strand exchange |
Mitocondrion
| Protein | Function |
|---|---|
| ATP synthase | ADP \(\rightarrow\) ATP |
3.RNA
| Acronym | denotation |
|---|---|
| mRNA | messenger RNA |
| noncoding RNAs | |
| rRNA | ribosomal RNA |
| tRNA | transfer RNA |
| snRNA | small nuclear RNA |
| miRNA | microRNA |
| siRNA | small interfering RNA |
| piRNAs | piwi-interacting RNAs |
| lncRNAs | long noncoding RNAs |
| Telomerase RNA |
4.Position of the DNA
| Position | Function |
|---|---|
| replication origins | first be opened |
5.Complex
- The DNA Replication Fork
6.Disease
| Cause | Disease |
|---|---|
| deficient mismatch proofreading | a type of colon cancer: HNPCC |
7.Techniques
| Technoques | Applications |
|---|---|
| autoradiography | eukaryotic chromosome replication: rate and direction |
| Atomic Force Microscope AFM | get 3D contour map of the surface resolueion: 0.1 nm in the vertical dimension 0.5~1.0 nm in the lateral dimension |
8.Models
- Lac repressor
- \(\text{strength of repression} = f(\text{distance between two binding sites})\)