LEHNINGER PRINCIPLES OF BIOCHEMISTRY
Fifth Edition
David L. Nelson and Michael M. Cox
© 2008 W. H. Freeman and Company
CHAPTER 24Information Pathways:Genes and
Chromosomes
Central Dogma: introduced by Francis Crickthe general pathways of information flow via replication, transcription, and
translation
1953 년 James Watson Francis Crick : DNA double helix 구조규명
Chapter 24. Genes and Chromosomes1. Chromosome 의 구성성분2. DNA supercoiling3. Chromosome 의 구조
• Genes: the fundamental unit of information in living systems– 생물학적 기능을 갖는 산물을 만드는데 필요한 정보를 암호화하는 DNA 의 일부
• Chromosomes: DNA 가 packaged 되어있는 구조 , 염색체 , contains thousands of genes and intergenic DNA
• Chromatin( 염색질 ): the entire complex of a eukaryotic chromosome, including DNA, chromosomal proteins and RNA
• Chromatid( 염색분체 ): one of the two daughter strands of a replicated chromosome( 복제결과 만들어진 자매염색 분체 )
• Genome: 생물의 최소한의 유전자군 ( 群 ) 을 가진 염색체의 한 세트 , 한 세포에 함유되는 DNA 의 총체
George Beadle, Edward Tatum: proposed a molecular definition of a gene in 1940 : one gene-one enzyme one
gene- one protein
FIGURE 24-2 Colinearity of the coding nucleotide sequences of DNA and mRNA and the amino acid sequence of a polypeptide chain.
1. Chromosomal elements• Genes are segments of DNA that code for polypeptide
chains and RNAs– Phenotype( 표현형 ): visible property (ex. Eye color)– George Beadle, Edward Tatum: proposed a molecular definition of
a gene in 1940– One gene-one enzyme– One gene-one protein– One gene-one polypeptide, tRNA, rRNA– Regulatory sequences provide signals of the beginning, the end of
gene, transcription, initiation points for replication, recombination
• E. coli– Completely sequenced, a circular DNA– Base pairs: 4,639,221 bp– Code: 4,300 genes for proteins, 115 genes for stable RNAcf) Human: 3.2 billion bp, 30,000 to 35,000 gene, 24 different
chromosomes
The size and sequence structure of DNA molecules
• Viral DNA molecules are relatively small.– Less genetic information– Genome (a single RNA or DNA) and protein coat– Retrovirus and DNA virus– Replicative forms: become circular and double-stranded
• Bacteria contain chromosomes and extrachromosomal DNA– More DNA than virus (100 times much E. coli vs bacteriophage )– A single double-stranded circular DNA– More tightly compacted tertiary structure than viral DNA– Circular DNA chromosome in the nucleoid– Extrachromosomal elements( 염색체외 DNA): plasmids free in cytosol
• 1,000 to 100,000 bp long• Carry generic information• Undergo replication (self propagation)• Antibiotic resistant cell ( 항생제의 남용 )• Cloning, recombinant DNA
FIGURE 24-1 Bacteriophage T2 protein coat surrounded by its single, linear molecule of DNA.
Bacteriophage T2 protein coat surrounded by single, linear molecule of DNA
The size and sequence structure of DNA molecules
• Eukaryotic cells contain more DNA than do prokaryotes.– More DNA than E.coli (yeast (2.6 배 ), fruit fly (35 배 ), human (700 배 ))– 50 genes/mm of human DNA vs. 2,500 genes/mm of E.coli DNA– 각세포는 2 m DNA x 1014 cells( 사람 ) = 2 x 1011 km
• 지구의 둘레 : 4 x 104 km, 태양까지의 거리 : 1.5 x 108 km– DNA compaction– Diploid (2n) number depends upon the species
• Human– 24 different types of chromosomes (22 matching pairs plus X and Y
set chromosomes) 25 배 이상의 길이차이 , 그러나 gene 의 수는 별차이 없음
• Organelles of eukaryotic cells also contain DNA.– Mitochondria and chloroplasts– Less than 0.1% of cell’s DNA in typical somatic cells– Much smaller than nuclear chromosomes (16,569 bp in human mtDNA)– Circular duplex, tRNA, rRNA, mitochondrial proteins– cpDNA(Chloroplast DNA): circular duplex, 120,000 to 160,000bp
Eukaryotic chromosomes are very complex• Intervening sequences (introns): nontranslated DNA segments in
genes (30% of human genome)– Exons: the coding segments (1.5%)– Few prokaryotic genes contain introns.– In higher eukaryotes: more introns than exons
• Moderately repetitive sequences (45% of human genome)– Derived from transposable elements (few hundreds to several thousands bp long)– Transposon: molecular parasites in host genome– Major role in human evolution: redistribution of other genomic sequences
• Highly repetitive sequences (3% of human genome)– Simple-sequenced DNA, simple sequence repeat (SSR)– Less than 10 bp long, millions times repeated per cell
• Satellites DNA: – Unusual base composition cause to migrate as satellite bands– Simple sequence DNA does not encode protein or RNA, associated with 2 important
structures– Centromere and Telomere– Artificial chromosome: centromere, telomeres, and DNA replication sequences
Type of sequences in human genome
Long interspersed elements6 to 8 kbpA few genes to catalyze transposition
Short interspersed elements100 to 300 bpAlu element (major)
1.5~11 kbpEvolutionally related to the retroviruses
Genes for proteins
Segmental duplicationAppear more than once
Simple-sequence repeats
Genes encoding RNAsRemnants of transposons?Unidentified: evolutionarily altered
FIGURE 24-8 Types of sequences in the human genome.
Centromere: functions during cell division as an attachment points for proteins that link the chromosomes to the mitotic spindle
yeast: 130 bp, rich in A=Thigher eukaryotes: longer, consists of simple-sequence DNATelomere: sequences at the ends of eukaryotic chromosomes that help stabilize the
chromosome•5’(TxGy)n, 3’(AxCy)n: ranges for x, y: 1 ~ 4, n: 20 ~ 100, 1500 in mammals•Telomerase: add repeated telomeric sequences•Linear DNA
Human artificial chromosomes (HACs) are being developed for somatic gene therapy
FIGURE 24-9 Important structural elements of a yeast chromosome.
2. DNA supercoiling
• Cellular DNA is highly compacted
• High degree of structural organization
• Folding mechanism– Packing DNA– Permit access to the information in the DNA
• Supercoiling
– It is an intrinsic property of DNA tertiary structure• Replication and transcription require a separation of DNA strands
• Topology: study of the properties of an object that do not change under continuous deformations– Continuous deformation: conformational changes– discontinuous deformation: involve DNA strand breakage
Most cellular DNA is underwound.• Closed-circular DNA: no breaks in either strand
– B-form structure– Relaxed than supercoiled– Supercoiling results when DNA is subject to the structural strain– DNA structure 는 strain 을 받아서 supercoil 을 형성하고 그 strain 은
세포에 의해서 조절된다 .– Underwinding
• Strain is a result of an underwinding.• Fewer helical turns (84/8=10.5 bp/turn 84/7=12 bp/turn)
– Deviation from the most stable DNA form (B form)– Thermodynamically strained– Separation (10bp: access to the information) or supercoiling
(compact)– Cells actively underwind DNA with the aid of enzymatic processes
• Only when the DNA is a closed circle• When it is bound and stabilized by proteins • So that the strands are not free to rotate about each other• Nick: relaxed state
FIGURE 24-16 Linking number applied to closed-circular DNA molecules.
underwinding
Separation or supercoiling
= -0.01 (1%)
Strands can be unraveled and separatedNo topological bond exists
2,100 bp/10.5 = 200
FIGURE 24-17 Negative and positive supercoils.
Topoisomers: 2 forms of a given circular DNA that differ only in a topological property such as linking number No effect on the number of vase pair, atoms
FIGURE 24-20 Visualization of topoisomers.
Changes in Lk catalyzed by Type I topoisomerases: change Lk in increments of 1
Supercoiled DNA is more compact
E. coli’s topoisomerases
• I through IV• Type I (topoisomerase I and III)
– generally relax DNA by removing negative supercoils (increasing Lk)
• Type II (topoisomerase II or DNA gyrase)– introduce negative supercoils (decrease Lk)– Uses the energy of ATP– Cleave both strands of DNA
• The degree of supercoiling of bacterial DNA is maintained by regulation of the net activity of topoisomerase I and II
Eukaryotic cell’s topoisomerases
• I and II• Type I (topoisomerase I and III) : 1 가닥을 끊어서 긴장을 품
• Type II (topoisomerase II and II) : 2 가닥 모두 끊어서 긴장을 품
– Cannot underwind DNA, although both can relax both positive and negative supercoils
– Cannot introduce negative supercoils– Negative supercoils in eukaryotic cells ?
→ 24.3 (slide 54)
FIGURE 24-22 Proposed mechanism for the alteration of linking number by eukaryotic type IIA topoisomerases. 1
<Quinolone antibiotics> Bacterial type II topoisomerase, DNA gyrase inhibitor
<Camptothecin derivatives> Eukaryotic type I topoisomerase inhibitor : anti-cancer
DNA compaction requires a special form of supercoiling
• Plectonemic (twisted and thread): 꼬인 실– The supercoils are right-handed in a negatively
supercoiled DNA molecules– Extended and narrow rather than compacted– Multiple branches– General structure of supercoiled DNA in solution
• Solenoidal– Tight left-handed turns– Negative supercoiling (both)– Underwound DNA (both)– Stabilized by protein binding– Readily interconvertible– Great degree of compaction
3. The structure of chromosome
• Chromosome ( 염색체 )– 유전정보의 저장고가 되는 nucleic acids– 색소로 진하게 염색되는 물체 ( 염색체 )– 유사분열 (mitosis) 사이 , 직전에 나타남 ( 농축됨 )
• Chromatin ( 염색질 ): chromosomal material– 정지되어 있는 분열하지 않는 세포상에서 염색체 물질
– 비정형이고 핵 중에 무질서하게 분산
– Consist of fibers containing protein and DNA, RNA (little)– DNA is tightly associated with Histones– Nucleosomes: structural unit
The beads: 8 histone molecules (2 copies of H2A, H2B, H3, H4)
Spacing: 200 bp (146 bp in histone core, remainders are linker DNA between nucleosome)
Histones are small, basic proteins
• Found in chromatic of all eukaryotes• Mr. 11,000 to 21,000• Very rich in the basic amino acids arginine and lysine (25%)• 5 major classes (Mr, amino acid composition)
– H3, H4: nearly identical in aa sequences in all eukaryotes: strict conservation of their functions
– H1, H2A, H2B: less sequence similarity among species• Variants forms by methylation, ADP-ribosylation,
phosphorylation, acetylation– Affect the net electric charge, shape, other properties of
histones, as well as the structural and functional properties of chromatin
– Regulation of transcription
Nucleosomes are the fundamental organizational units of chromatin
• The compaction• Beads-on-a-string arrangement: complexes of histones
and DNA: nucleosome– The beads: 8 histone molecules (2 copies of H2A, H2B,
H3, H4)– Spacing: 200 bp (146 bp in histone core, remainders are
linker DNA between nucleosome)– Preferential degradation of the linker DNA release
histones containing 146 bp DNA– 8 histone molecules with the DNA wrapped in a left-
handed solenoidal supercoil
FIGURE 24-28 Chromatin assembly.
Chromatin assembly
Relaxed, closed circular DNA
Binding of a histone core induces one negative supercoil and one positive supercoil
Relaxation by topoisomerase
Nucleosomes are packed into successively higher-order structures
• Wrapping DNA around a nucleosome core: 7-fold compaction
• Nucleosome packing– 30 nm fiber– H1 per nucleosome core required for packing– transcription region: less-ordered state, little H1– 2nd level of chromatin organization: 100-fold
compaction of the DNA• Nuclear scaffold: separated by loop of DNA with 20,000 to
100,000 bp• Additional layers of organization: coils upon coils upon
coils……………………
FIGURE 24-30 The 30 nm fiber, a higher-order organization of nucleosomes.
The 30 nm fiber, a high-order organization of nucleosomes
FIGURE 24-32 Loops of chromosomal DNA attached to a nuclear scaffold.
separated by loop of DNA with 20,000 to 100,000 bp
Active chromatin: sensitive to digestion by nuclease: hypersensitive site >>>Euchromatin
Inactive chromatin: densely packed >>>> heterochromatin: constitutive( always condensed) facultative ( at times condensed)
Condensed chromosome structures are maintained by SMC proteins
• 3rd major class of chromatin proteins• SMC proteins: structural maintenance of chromosomes• 5 distinct domains
– N, C: part of ATP hydrolytic site– 2 regions of -helical coiled-coil motifs– A hinge domain
• Dimer, V-shaped• From bacteria to human• Eukaryotes
– Cohesins: linking sister chromatids after replication – Condensins: condensation of chromosomes during
mitosis, condensin binding cause DNA overwound (positive supercoil)
Bacterial DNA is also highly organized
• Bacterial DNA is compacted in a structure, called the Nucleoid– Attached at one or more points to the inner surface of
the plasma membrane– Scaffoldlike structure– Organize the circular chromosome into a series of
looped domains– HU (Mr, 19,000): histonelike proteins– Relatively dynamic, more ready access to its genetic
information
Single Nucleotide Polymorphism (SNP)
• Common DNA sequence variations among individuals in genome wherein the least frequent allele has an abundance of 1% or greater.
• Make up about 90% of all human genetic variation • Occurs every 100 bases along the 3-billion-bases human
genome (dbSNP 132 version : 30,443,445 SNPs)• Some SNPs are reported to be highly related to diseases
or influence cells response to a drug
Person 1….ATCCTGTACCTACGTGTACAATAGTA…..CTGATCATCTCTATGGG….Person 2….ATCCTGTTCCTACGTGTACAATAGTA…..CTGATCATCTCTATGGG….Person 3….ATCCTGTACCTACGTGTACAATAGTA…..CTGATCAGCTCTATGGG….
SNP1 SNP2
Epigenetics and Different Aspects of Life
• Development of multicellular organism• Environment-organism interaction For examples: Nutrition supplements and environmental toxins
Image: Randy Jirtle
• Pathogenesis of diseases
SNP Types
regulatory region SNP
intron SNP Coding region SNP
Synonymous SNP
Intergenic SNP
Gene Gene
Amino acid Substitution
No amino acid substitution
Possible protein function Change
Non-synonymous SNP
Splicing region SNP
Genome wide association study
• An examination of most of the SNPs of different individuals of a particular species to see how much the SNPs vary from individual to individual.
• Goal : Uncover the genetic basis of a given disease.• Basic Idea : A rather vague idea of a study design that
involves genotyping cases and controls at a large number of SNP markers spread throughout the genome. Look for associations between the genotypes at each locus and disease status
Case Control
Comparison of SNP Genotype frequency
Epigenetics
• Epigenetics refers to the study of changes in the regulation of gene activity and expression that are not dependent on gene DNA sequence.
• While epigenetics often refers to the study of single genes or sets of genes, epigenomics refers to more global analyses of epigenetic changes across the entire genome.
DNA Methylation and Other Human Diseases
-- Imprinting Disorder:• Beckwith-Wiedemann syndrom (BWS)• Prader-Willi syndrome (PWS)• Transient neonatal diabetes mellitus (TNDM)
-- Repeat-instability diseases• Fragile X syndrome (FRAXA)• Facioscapulohumeral muscular dystroph
-- Defects of the methylation machinery• Systemic lupus erythemtosus (SLE)• Immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome
SIRT1 activator: Resveratrol analogy Resveratrol is found in grapes, wine, grape juice, and berries of Vaccinum species including blueberries, bilberries, raspberries( 覆盆子 )and cranberries. Cell energy
demand [ATP]/[AMP]
Activationde l’ AMPK Resveratrol
SIRT 1
FOXO PPARPGC-1 α
EnergeticMetabolism
Release of fattyacids from adipose
tissue
Calorie Restriction
Food Serving Total resveratrol (mg)Peanuts (raw) 1 c (146 g) .01-0.26Peanuts (boiled) 1 c (180 g) .32-1.28Peanut butter 1 c (258 g) .04-.013Red grapes 1 c (160 g) .24-1.25
(SIRT1: histone deacetylase, HDAC 의 일종 )
Deacetylation 시켜 활성유지
요약
1. Gene, central dogma, prokaryote, eukaryote 2. Intron, exon, repetitive sequence3. Centromere, telomere4. Supercoiling - topoisomer - type , topoisomerase, inhibitorsⅠ Ⅱ5. Nucleosome, Euchromatin/heterochromatin6. 30nm chromatin fiber 7. SMC protein8. SNP 9. Epigenetics/epigenome: DNA methylation, histone modification