agricultural molecular biology 555522. agricultural molecular biology teaching team ดร....
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Agricultural Molecular Biology
555522
Agricultural Molecular BiologyTeaching Team
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Agricultural Molecular BiologyCourse Structure
• Credit 3-0 : 45-hour program• Class schedules : Monday 9.00-10.30
Wednesday 9.00-10.30
CAB Lecture room 3rd floor• Evaluation :
– Exam I, II, III 75%, TBA– Presentation 10%– Paper 10%– Class participation 5%
• Grading system : Score-dependent
Agricultural Molecular BiologyCourse Textbooks
• Genes VII, 2000. By Benjamin Lewin.– 5 Reserved books, KPS library
• Molecular Biology, International Edition. 1999. By Weaver RE.
• Genomes, 1999. By TA Brown
What is molecular biology?
• A study of gene structure and function at the molecular level
• Molecular biology grew out of the disciplines of genetics and biochemistry
A brief history
• Transmission of genetics– Mendel’s law of inheritance– Chromosome theory of inheritance– Genetic recombination and mapping– Physical evidence for recombination
• Molecular genetics– Discovery of DNA– Composition of genes– Relationship between genes and proteins– Activities of genes
Transmission of genetics 1856 Gregor Mendel: inheritance of 7 traits in garden pea
Mendel’s laws of inheritance >> principle of segregation
• Genes exist in different forms called alleles.• One allele can be dominant over the other.• Mendel’s work: yellow seed > green seed
parents yellow x green
F1
yellow selfed
F2
3 yellow : 1 green
Mendel’s laws of inheritance >> principle of independent assortment
• 7 genes operated independently• Combinations of 2 different genes 9:3:3:1
Chromosome theory of inheritance
• 1900 rediscovery Mendel’s findings• First chromosome theory:
– Thomas Hunt Morgan: fruit fly (Drosophila melanogaster)
- -red eyed x white eyed
- most red eyed F1
red-eyed males x red-eyed females
1/4 white-eyed males + no white-eyed females
• Eye color is sex-linked, X chromosome– male has 1 copy, female has 2 copies
• Genes are located on chromosome : locus• Diploid organisms have 2 copies of chromosomes
– homozygous and heterozygous– genotype– phenotype : wild-type vs mutant
Genetic recombination and mapping
• Genes on separate chromosome behave independently, same chromosome behave as if they are linked
• Genes on same chromosome not perfect linked• Eye color and miniature wing on X chromosome are 65.5
% linked, with new combination ‘recombinants’• Answer is recombination process, a crossing over betwee
n homologous chromosomes during meiosis• Sturtevant: mathematical relationship between the dista
nce of genes and the recombination frequency• Barbara McClintock : physical evidence for recombinatio
n in maize chromosomes
Molecular genetics
• DNA discovery : 1869 Friedrich Miescher - nuclein– deoxyribonucleic acid (DNA)– ribonucleic acid (RNA) and protein
• Composition of genes– DNA or RNA or protein– Avery proved it was DNA– Bacteria transformation
• virulent dead cells + avirulent living cells• Relationship : genes and protein
Molecular genetics
• Relationship : genes and protein– How do genes work?– Human disease alcaptonuria -- black pigment in urine– Defective enzyme– A gene responsible for enzyme (protein) production
• Activities of genes– How do genes work?– Genes replicate faithfully– Genes direct production of RNAs and proteins– Genes accumulate mutations and allow evolution
Replication
• 1953 Watson and Crick• DNA structure is double helix• 4 bases composition : A, G, T and C
– A - T, G- C• semiconservative replication
Production of polypeptides
• Gene product is either RNA or polypeptides– gene expression
• Transcription : a single copy of DNA strand (RNA)• Translation : protein production
– mRNA carries genetic code to ribosomes– genetic code = codon consisting of 3 bases
• 61 amino acids, 3 stop signals• Accumulate mutations
– one base change -- sickle cell disease– deletions or insertions– transposon
Gene cloning
• Isolate genes and place them in new organisms• Benefits :
– raw materials for studies in molecular biology– protein product ie human insulin– Bt cotton
Genome structure and organisation>>what is genome?
• Genome is the entire DNA content of a cell, including all of the genes and all the intergenic regions
• Most genome are made of DNA• 2 types of living organisms
– prokaryotes: cells lack extensive internal compartmetns
– eukaryotes: cells contain membrane-bound compartments ie. Nucleus, mitochondria, chloroplast
• animals, plants, fungi and protozoa are eukaryotes
Why are genome projects important
Why are genome projects important?
• Genome sequences are the key to the continued development --opens the way to a comprehensive description of the molecular activities of living cells and the ways in which these activities are controlled
• Gene catalog -- isolation and untilisation of important genes
• Additional benefits -- study role of noncoding DNA• Challenge of unknown
Genomes of eukaryotes
• Eukaryotic genome is split into 3 components– nuclear genome– mitochondrial genome– chloroplast genome
• made up of 2 components: nuclear and mitochondria
Human genome
Human genome
• nuclear genome: – 3000 Mb DNA – linear genome divided into 24 (22 autosomes + 2
sex chromosome, X and Y)– shortest 55 Mb and longest 250 Mb
• mitochondrial genome:– circular DNA 16,569 bp
Human genome
• immensity of human genome– analog with normal font size --60 nt = 10 cm– genome sequence stretch for 5,000 km
Nuclear genome
• Genome size ranges <10 Mb to >100,000 Mb
• size broadly coincides with organism complexity
• larger genome --high repeats
Nuclear genome
• Split into a set of linear DNA molecules -chromosomes• chromosome number not related to organism features
Where are genes in a genome?>>Human EST map --expressed sequence tags
Families of genes
• Multigene family --groups of genes of identical or similar sequence– rRNA genes : 5S, 28S, 5.8S and 18S– globin gene families
• alpha-globin family, on chr#16• beta-globin family, on chr#11
• Supergene family– globin supergene family --alpha and beta evolve
from a single ancestral globin gene
Pseudogenes
• Genes which for one reason or another have become nonfunctional– conventional
pseudogenes --inactivation by mutation ie. Create termination codon within coding region
– processed pseudogenes -- abnormality during gene expression
Organelle genomes
• Mitochondria and chloroplasts• Extra chromosomal genes --unusual inheritance patterns• Most mitochondrial and chloroplast genomes are circular
Genetic content of organelle genomes
• Mitochondria display greater variability– number of genes : 12-92– genes for mitochondrial rRNAs, protein components
for respiratory chain• Chloroplasts are less variable
– gene number ~ 200– coding for rRNAs, tRNAs and ribosomal proteins and
proteins involved in photosynthesis
Prokaryotic genome
• Physical structure: size < 5 Mb• Genome is contained in a single circular DNA molecule
in nucleoid• Circular E. coli chromosome circumference is 1.6 mm,
while cell is 1x2 um
Supercoiling
Prokaryotic genome
• Plasmid: small piece DNA, often circular, coexist with main chromosome in a bacteria cell
• plasmids carry genes not present in main chromosome
Prokaryotic genome
• Controversy: should plasmid be part of genome?– E. coli : main chromosme 4.6 Mb+ few kb of plasmid
DNA which are not essential– Borrelia burgdorferi: 910 kb main chromosome
carrying 853 genes + 17 linear and circular plasmids of 533 kb with 430 genes, some of which are essential
Prokaryotic genome
• Genetic organisation: bacterial genomes have compact genetic organisations with little space between genes
Genetic organisation• Operons: an operon is a group of genes located
adjacent to one another in the genome• All genes in an operon are expressed as a single unit
Operon controversy
• Most cases, genes in an operon are functionally related, coding for a set of proteins involved in a single biochemical activity
• Some species, genes in an operon rarely have any biochemical relationship
Repetitive DNA
• Repetitive DNA found in all organisms, in some including humans shows substantial composition
Repetitive DNA
• There are various types of repetitive DNA– tandemly repeated
DNA– interspersed genome-
wide repeats• Tandemly repeats:
– common features of eukaryotes
– also called satellite DNA
Satellite DNA
• Satellite bands in density gradient made up of long series of tandem repeats, hundreds kb
• A genome can contain different types of satellites• Alphoid DNA: one type of satellites in centromere• Minisatellites: form clusters up to 20 kb with repeat
units up to 25 bp – telomeric DNA --important function in DNA
replication
Satellite DNA
• Microsatellites: shorter, usually < 150 bp with repeat unit 4 bp or less– although short, there are many --useful as markers
for mapping– in human, CA repeats make up 0.5% og genome or
15 Mb; A repeats 0.3%– function is mysterious, but useful to geneticists as
they are variable• number of repeats different in different members
of a species due to slippage during DNA replication --insertion or deletion
• No 2 humans have exactly the same combination of microsatellite alleles
Interspersed genome-wide repeats
• Interspersed repeats arise from transposition• Most repeats have inherent transpositional activity