Section 3: Molecular Biology Bilingual teaching as a reform Is a stretch of dynamic biochemistry Focus on the biosynthesis of 3 macromolecules: DNA: replication RNA: transcription Protein: translation
Jan 20, 2016
Section 3:
Molecular Biology
Bilingual teaching as a reform
Is a stretch of dynamic biochemistry
Focus on the biosynthesis of 3 macromolecules:
DNA: replication
RNA: transcription
Protein: translation
Chapter 29 An Overview of Genetic InformationChapter 29 An Overview of Genetic Information
Which are macromolecules?
Life is produced by the metabolism of macromolecules
The function of life is executed by proteins, which encoded by nucleic acid
The second genetic codon
The second genetic codon……
生物进化的 C 值矛盾 (C value paradox of nucleotide)
The total amount of DNA in the genome of haploid
is a characteristic of each living species known as its
Maximum C value (单倍体基因组总 DNA 的含量 )
最大 C 值 (Maximum C value)
The total amount of DNA for encoding the genes
information is termed its Minimum c value (编码基
因信息的总 DNA含量)
最小 C 值 (Minimum c value)
C value paradox of nucleotide
霉菌藻类
G+细菌G-细菌
显花植物鸟类哺乳类爬行类两栖类硬骨鱼类软骨鱼类赖皮类甲壳类昆虫类软体动物蠕虫类
真菌
枝原体
A Is not linearly correlative with evolution extent
B The standard deviation varies in the same genus
C C value is far from c value.
( Euk. 人体 c = C/10)
( Prok. Φx174 c > C )
Eukaryote DNA chromosomes
( 2C )( 2N)
两栖鲵 168.0 pg(10-12g) 24
肺鱼 100 38
蝾螈 85.3 24
警蛙 28.2 24
牛 6.4 60
人 6.4 46
绵羊 5.7 54
果蝇 0.2 8
贝母 196.7 24
豌豆 28 12
玉米 11 20
Prokaryote DNA
( C)
Salmonella 0.0143 pg
E.coli 0.0040
T2 0.00022
λ 0.0000055
ΦΧ174 0.000005
Repeat sequence
单一序列长度愈小(重复度愈大) kinetic complexity(K.C.)愈小 Cot(1/2)值小(复性愈快)
poly(A ) K.C. = 1
Cot(1/2) = 2 × 10-6
T4 DNA K.C. = 1.7 × 106
Cot(1/2) = 0.3
E.coli DNA K.C. = 4.2×106 bp
Cot(1/2) = 9
DNA的复杂度:单倍体细胞基因组中非重复序列的碱基对数
DNA as a major genetic material
Experiment 1:
Marked protein by 35S
Marked DNA by 32P
Experiment 2:
35S can not enter the new cells.
However, 32P was found in the new cells.
German Fraenkel
Extract the RNA and protein of the virus individually.
Put them into the surface of the healthy leaves.
RNA caused the disease.
While protein can not.
Conclusion: Genetic material is RNA not protein.
Experiment 3:
Gregory Johann Mendel (1822-1884)
7 traits
phenotype
But where is the “genetic factor”?
Founder of modern genetics: Thomas Hunt Morgan
Tied genetic factor (gene) with chromosomes.
Sexual linkage by drosophila is regarded as the third discover in genetics because it brings together a specific gene and chromosomes.
If 2 genes are near in the same chromosome, maybe linked heredity.
If far, maybe exchanged-heredity.
Opportunity for exchange can be viewed as the distance of 2 genes
Essence of the genes
One gene, one enzyme
One peptide, one gene
Trait——protein——gene: Forward Biology
Gene——protein——trait : Reverse Biology
DNA
Mostly in chromosome
Semi-autonomous organelle or
plasmid
Nucleus Cytoplast
Heredity
Category of genetic materials
In most cases DNA works as genetic material
RNA works in some viruses
Protein?
Functional diversity of RNA
Transferring and processing genetic information
Focused on protein synthesis
Messenger RNA
Transfer RNA
Ribosome RNA
RNA processing genetic information
General process
Recoding sequence
CutTrimmingAddingModificationIsomerization
Splicing
Editing
Recoding
Alternative transcript
1.Correcting tRNA and the second system of genetic codon
2.Sometimes tRNA will transfer an amino acid in nonsense mutations.
赭石突变( UAA)琥珀突变( UAG)乳白突变( UGA )
Recoding
nonsense mutations
RNA interfering干涉(干扰, RNAi)
The small double-strand RNA can inhibit gene expression.
C. Elegans or petunias (牵牛花 )?
More effective than Antisense RNA
Models
NatureDecipheringFeatureEffect of mutation
Universality
ORFs
Overlapping genes
Genetic codon
Nature
1. Genetic code is a triplet code
(three nucleotide encode one amino acid)
The way in which the nucleotide sequence in nucleic acids specifies the amino acid sequence in proteins.
The triplet codons are nonoverlapping and comma-less.
------UCU UCC CGU GGU GAAUCU UCC CGU GGU GAA------
2. Genetic code is degenerate :
Only 20 amino acids are encoded by 4 nucleotides in triplet codons (43 =64 of amino acids could potentially be encoded). Therefore, more than one triplet are used to specify a amino acids, and the genetic code is said to be degenerate, or to have redundancy.
Deciphering
System A: cell-free protein synthesizing system from E. coli
1. cell lysate treated by DNase to prevent new transcription
2. Add homopolymeric synthetic mRNAs [poly(A)] + 19 cold (non-labeled) and one labeled aminoacids
3. In vitro translation4. Analyze the translated polypeptides
poly(U) ---UUU--- polyphenylalanine
poly(C) ---CCC--- polyproline
poly(A) ---AAA--- polylysine
poly(G) --- did not work because of the complex secondary structure
Random co-polymers (e.g. U and G Random co-polymers (e.g. U and G in the same RNA) were used as in the same RNA) were used as mRNAs in the cell-free system to mRNAs in the cell-free system to determine the codon for many determine the codon for many amino acids.amino acids.
Features
Synonymous codons: 18 out of 20 amino acids have more than one codon
to specify them, causing the redundancy of the genetic code.
the third position:
pyrimidine ----synonymous (all cases)
purine ----synonymous (most cases)
the second position:
pyrimidine ----hydrophobic amino acids
purine -----polar amino acids
Effect of Mutation
1. Transition: the most common mutation in nature
changes from purine to purine, or pymidine to pymidine
At third position: no effect except for Met Ile; Trp stopsecond position: results in similar chemical
type of amino acids.
2. Transversions: purine pymidine At third position: over half have no
effect and result in a similar type of amino acid. (Example: Asp Glu)
At second position: change the type of amino acid.
In the first position, mutation (both transition and transvertion) specify a similar type of amino acid, and in a few cases it is the same amino acid.
Thus, natural triplet codons are Thus, natural triplet codons are arranged in a way to minimize arranged in a way to minimize the harmful effect of an the harmful effect of an mutation to an organism. mutation to an organism.
Summary
简并性 :64种密码子决定 20种氨基酸,重复,同义密码子
摆动性(变偶性):反密码子的 3个碱基与密码子反向互补,前两个碱基严格互补,第三个可以摆动
普遍性:生物体普遍适用
偏爱性:不同生物体(线粒体)使用何种同义密码子有偏爱
Universality
• The standard codons are true for most organisms, but not for all.
Codon Usual meaning Alternative Organelle or organism
AGA AGG Arg Stop,Ser Some animal mitochondria
AUA Ile Met Mitochondria
CGG Arg Trp Plant mitochondria
CUN Leu Thr Yeast mitochondria
AUU GUG UUG
Ile Val Leu Start Some protozoans
UAA UAG Stop Glu Some protozoans
UGA Stop Trp Mitochondria,mycoplasma
ORFs
Open reading frames (ORFs) are suspected coding regions starting with ATG and end with TGA,TAA or TAG identified by computer.
When the ORF is known to encode a certain protein, it is usually referred as a coding region.
I coupled with U,A and C
Which codon can be recognized by Anticodon IGC?
Processing of RNA
Only the mature RNA could be translated.
The precursor of mRNA is called heterogeneous nuclear RNA, (hnRNA), which needs be processed.
Processing: Capping in 5 , end
Poly A in 3 , end
Cutting intron
Linked exon
m7G加在 5 ,端:
免受酶切
促进启始蛋白质合成