Molecular Biology 2M03 Lecture Notes PDF

Molecular Biology 2M03 Instructor: Dr. Fei Geng Introduction • Hereditary factors consist of DNA and reside on chromosomes. • The collective body of genetic information in an organism is called the genome. genome books DNAE It - yo booksiche Chrmosome A pht Fanc us genome sch Yer X DN...

Molecular Biology 2M03 Instructor: Dr. Fei Geng Introduction • Hereditary factors consist of DNA and reside on chromosomes. • The collective body of genetic information in an organism is called the genome. genome books DNAE It - yo booksiche Chrmosome A pht Fanc us genome sch Yer X DNA Overview of early discoveries on the nature of the gene 10.1 The Concept of a Gene as a Unit of Inheritance (1) • Mendel’s work became the foundation for the science of genetics. • He established the laws of inheritance based on his studies of pea plants. The Concept of a Gene as a Unit of Inheritance (2) 1. Characteristics of organisms are governed by units of inheritance called genes. a) Each trait is controlled by two forms of a gene called alleles. b) Alleles could be identical or nonidentical. c) When alleles are nonidentical, the dominant allele masks the recessive allele. C & requires that only of the two one alleles be present to express the trait does not produce when only a trait one copy at is all present The Concept of a Gene as a Unit of Inheritance (3) -- 2. A reproductive cell (gamete) contains one gene for each trait. a) Somatic cells arise by the union of male and female gametes. b) Two alleles controlling each trait are inherited; one from each parent. & 3. The pairs of genes are separated (segregated) during gamete formation. 4. Genes controlling different traits segregate independently of each (independent assortment). 10.2 Chromosomes: The Physical Carriers of Genes (1) • The Discovery of Chromosomes – Chromosomes were first observed in dividing cells, using the I light microscope. – Chromosomes are divided equally between the two daughter cells during cell division. – Chromosomes are doubled prior to cell division. O - Cellular process in the roundworm following fertilization Chromosomes: The Physical Carriers of Genes (2) • Chromosomes as the Carriers of Genetic Information – Chromosomes are present as pairs of homologous chromosomes. – During meiosis, homologous chromosomes associate and form a bivalent; then separate into different cells. – Chromosomal behavior correlates with Mendel’s laws of inheritance. - O Homologous chromosomes Chromosomes: The Physical Carriers of Genes (3) & • The chromosome as a linkage group – Genes that are on the same chromosome do not assort independently. – Genes on the same chromosome are part of the same linkage group. – The traits analyzed by Mendel occur on different chromosomes. - & - Chromosomes: The Physical Carriers of Genes (4) • Genetic Analysis in F Drosophila – Morgan was the first to use fruit flies in genetic research. – Morgan only had available wild type flies but once he developed his first mutant, it became a primary tool for genetic research. – Mutation was recognized as a mechanism for variation in populations. – Studies with Drosophila confirmed that genes reside on chromosomes. - Drosophila as a genetic tool Chromosomes: The Physical Carriers of Genes (5) • Crossing Over and Recombination – Linkage between alleles on the same chromosome is incomplete. – Maternal and paternal chromosomes can exchange pieces during crossing over or genetic recombination. && Crossing over in Drosophila Chromosomes: The Physical Carriers of Genes (6) • Crossing over and recombination – Percentage of recombination between a pair of genes is constant. – Percentage of recombination between different pairs of genes can be different. – The positions of genes along the chromosome (loci) can be mapped. – Frequency of recombination indicates distance, and increases as distance increases. && - - Chromosomes: The Physical Carriers of Genes (7) • Mutagenesis and Giant Chromosomes - – Exposure to a sublethal dose of X-rays increases the rate of spontaneous mutations. – Cells from the salivary gland of Drosophila have giant polytene chromosomes. – Polytene chromosomes have been useful to observe specific bands correlated with individual genes. – “Puffs” in polytene chromosomes allow visualization of gene expression. Polytene chromosomes 10.3 The Chemical Nature of the Gene (1) • DNA is the genetic material in all organisms. • The Structure of DNA: – The nucleotide is the building block of DNA. • It consists of a phosphate, a sugar, and either a pyrimidine or purine nitrogenous base. • There are two different pyrimidines: thymine (T) and cytosine (C). • There are two different purines: adenine (A) and guanine (G). The chemical structure of DNA The chemical structure of DNA The Chemical Nature of the Gene (2) • Nucleotides have a polarized structure where the ends are called 5’ and 3’ . • Nucleotides are linked into nucleic acids polymers: – Sugar and phosphates are linked by 3’,5’phosphodiester bonds. – Nitrogenous bases project out like stacked shelves. The Chemical Nature of the Gene (3) • Chargaff established rules after doing base composition analysis: – Number of adenine = number of thymine – Number of cytosine = number of guanine – [A] + [T] ≠ [G] + [C] O The Chemical Nature of the Gene (4) • The Watson-Crick Proposal – The DNA molecule is a double helix. • DNA is composed of two chains of nucleotides. • The two chains spiral around each other forming a pair of right-hand helices. • The two chains are antiparallel, they run in opposite directions. • The sugar-phosphate backbone is located on the outside of the molecule. • The bases are inside the helix. - & & sugar - phosphate backbone - outside bases -> inside The double helix The Chemical Nature of the Gene (5) • The Watson-Crick Proposal (continued) – The DNA is a double helix • The two DNA chains are held together by hydrogen bonds between each base. E • The double helix is 2 nm wide. •Pyrimidines are always paired withpurines. • Only A-T and C-G pairs fit within double helix. • Molecule has a major groove and a minor groove. • The double helix makes a turn every↳ 10 residues. • The two chains are complementary to each other. ⑧ & - - The double helix (continued) The Chemical Nature of the Gene (6) • The Importance of the Watson-Crick Proposal & – Storage of genetic information. – Replication and inheritance. – Expression of the genetic message. - - Three functions of the genetic material The Chemical Nature of the Gene (7) • DNA Supercoiling – DNA that is more compact than its relaxed counterpart is called supercoiled. & The Chemical Nature of the Gene (8) underwound negative -> • DNA Supercoiling (continued) – Underwound DNA is negatively supercoiled, and overwound DNA is positively supercoiled. – Negative supercoiling plays a role in allowing chromosomes to fit within the cell nucleus. - overwound -> positive The Chemical Nature of the Gene (9) • DNA Supercoiling (continued) – Enzymes called topoisomerases change the level of DNA supercoiling. – Cells contain a variety of topoisomerases. & - - • Type I – change the supercoiled state by creating a transient break in one strand of the duplex. • Type II – make a transient break in both strands of the DNA duplex. ⑧ Type I- Type /I -> change make the a supercoiled transient state break ⑳ by creating inth strands a transist break DNA topoisomerases DNA topoisomerases 10.4 The Structure of the Genome (1) • The genome of a cell is its unique content of genetic information. • The Complexity of the Genome – One important property of DNA is its ability to separate into two strands (denaturation). I The Structure of the Genome (2) • DNA Renaturation I – Renaturation or reanneling is when singlestranded DNA molecules are capable of reassociating. – Reanneling has led to the development of nucleic acid hybridization in which complementary strands of nucleic acids form different sources can form hybrid molecules. - - The Structure of the Genome (3) • The Complexity of Viral and Bacterial Genomes – The rate of renaturation of DNA from bacteria and viruses depends on the size of their genome. - & - rate of renaturation of DNA+ size of their genome The Structure of the Genome (4) • The Complexity of the Eukaryotic Genome – Reanneling of eukaryotic genomes shows three classes of DNA: • Highly repeated • Moderately repeated • Nonrepeated The Structure of the Genome (5) • Highly Repeated DNA Sequences – represent about 1-10% of total DNA. & – Satellite DNAs – short sequences that tend to evolve very rapidly. – Minisatellite DNAs – unstable and tend to be variable in the population; form the basis of DNA fingerprinting. – Microsatellite DNAs – shortest sequences and typically found in small clusters; implicated in genetic disorders. - - - test & DNA fingerprinting Fluorescence in situ hybridization and localization of satellite DNA The Structure of the Genome (6) • Moderately Repeated DNA Sequences – Repeated DNA Sequences with Coding Functions – include genes that code for ribosomal RNA and histones. – Repeated DNA Sequences that Lack Coding Functions – do not include any type of gene product; can be grouped into two classes: SINEs or LINEs. & & • Nonrepeated DNA Sequences – code for the majority of proteins. Chromosomal localization of nonrepeated DNA The Human Perspective: Diseases That Result from Expansion of Trinucleotide Repeats (1) • Mutations occur in genes containing a repeating unit of three nucleotides. • The mutant alleles are highly unstable and the number of repeating units tends to increase as the gene passes from parent to offspring. • Type I disease are all neurodegenerative disorders resulting form expansion of CAG trinucleotides. & Trinucleotide repeat sequences and human disease The Human Perspective: Diseases That Result from Expansion of Trinucleotide Repeats (2) • Huntington’s disease (HD) result from ≥ 36 glutamine repeats in the huntingtin gene. • The molecular basis of HD remains unclear but it is presumed that expanded glutamine repeats are toxic to brain cell. • Type II diseases arise from a variety of trinucleotide repeats, and are present in parts of the gene that do not code for amino acids (i.e. fragile X syndrome). 10.5 The Stability of the Genome (1) • Whole Genome Duplication (Polyploidization) – Polyploidization (or whole genome duplication) occurs when offspring receive more than two sets of chromosomes from their parents. - & • Could be the result of hybrids from closely related parents. • Could result fromduplicate chromosomes not separated in embryonic cells. - - A sample of agricultural crops that are polyploid The Stability of the Genome (2) • Duplication and Modification of DNA Sequences – Gene duplication occurs within a portion of a single chromosome. – Duplication may occur by unequal crossing over between misaligned homologous chromosomes. – Duplication has played a major role in the evolution ofmultigene families. - Unequal crossing over between duplicated genes The Stability of the Genome (3) • Evolution of Globin Genes – The globin gene family includes hemoglobin, myoglobin, and plant leghemoglobin. – Ancestral forms have given rise to recent forms by duplication, gene fusion, and divergence. – Some sequences, called pseudogenes, resemble globin genes but are nonfunctional. - - - E - globin + nonfunctional A pathway for the evolution of globin genes The Stability of the Genome (4) • “Jumping Genes” and the Dynamic Nature of the Genome – Genetic elements are capable of moving within a chromosome (transposition). – Those mobile elements are called transposable elements. transposable -- - O & elements - transposition The Stability of the Genome (5) • Transposition – Only certain sequences can acts as transposons, but these insert into target sites randomly. - • It requires the enzyme transposase to facilitate insertion of transposons into target site. • Bacterial trasnposition occurs by replication of the transposable element, followed by insertion. - ⑤) Transposition in bacteria The Stability of the Genome (6) • Transposition (continued) – Integration of the element creates a small duplication in target DNA, which serves as a “footprint” to identify sites occupied by transposable elements. – Retrotransposons use an RNA intermediate which produces a complementary DNA via reverse transcriptase; viruses such as HIV use this mechanism to replicate their genome. - Pathways in the movement of transposable elements The Stability of the Genome (7) • The Role of Mobile Genetic Elements in Evolution & – Some moderately repeated sequences in human DNA (Alu and L1) are transposable elements. – Possible evolutionary roles: & • Rearrangement of the genome • Regulation of gene expression • Production of new genes - - 10.6 Sequencing Genomes: The Footprints of Biological Evolution (1) • The genomes of hundreds of organisms have been sequenced. • In 2004 the “finished” version of the human genome was reported. – It contains about 20,000 genes. – Alternate splicing of messenger RNA may account for several proteins from one gene. – Post-translational modifications also account for different protein functions. Genome comparisons Sequencing Genomes: The Footprints of Biological Evolution (2) • Comparative Genomics: “If It’s Conserved, It Must Be Important” – DNA that is similar among related organisms is considered to be important, even when the precise role is still unclear. – Some important DNA in humans may have a recent origin Small segments of DNA are highly conserved between humans and related species Sequencing Genomes: The Footprints of Biological Evolution (3) • The Genetic Basis of “Being Human” – By focusing on conserved sequence, we can learn about traits we share with other species. & • The gene FOXP2 in human differs very little from that in chimps, and is called the “speech gene”. • Another gene is HAR1, which also differ little between humans and chimps and its function is unknown. • The gene AMY1 encodes the enzyme amylase and its frequency is remarkably different between humans and chimps. - - Duplication of the amylase gene during human evolution Sequencing Genomes: The Footprints of Biological Evolution (4) • Genetic Variation within the Human Species Population – The genome varies among different individuals due to genetic polymorphisms. • DNA Sequence Variation – The most common variability among humans is at the single nucleotide difference. – These sites are called single nucleotide polymorphisms (SNPs). Sequencing Genomes: The Footprints of Biological Evolution (5) • Structural Variation – Segments of the genome can change, and these changes may involve large segments of the DNA (structural variants). – Recent studies indicate that intermediatesized variants are more common than previously thought. Structural variants