Chapter 8 Notes PDF

Preview

Summary

These notes cover lectures from chapter 8. The textbook used is molecular biology, 7th edition ...

Description

Chapter 8: Genome Structure Pages 199-208 Key Vocabulary: -

-

-

-

Chromosomes: Each DNA molecule and its associated protein Chromatin: A given region of DNA with its associated protein Histones: basic associated proteins Non-histone proteins: Proteins include numerous DNA- binding proteins that regulate replication, repair, recombination, and transcription of cellular DNA Haploid: contains single copy of each chromosome that are involved in sexual reproduction Diploid: contain 2 copies of each chromosomes, mostly in eukaryotic cells Nucleosomes: Histones forms a regular association with DNA to fold compact structures by forming nucleosomes Nucleoid: central region in prokaryotic cell that contains the chromosomes and has no surrounding membrane Plasmids: prokaryotes carry one or more smaller independent circular DNA which are plasmids Homologs: One being derived from each parent Polyploid: have more than 2 copies of each chromosomes Nucleus: membrane-bound organelle where chromosomes are found Intergenic sequences: 2 factors that contribute to decrease gene density in eukaryotic: increase in gene size and increase inn DNA between genes Introns: Non-protein coding regions found in eukaryotic cells RNA splicing: RNA during transcription removes introns Regulatory Sequences: one of the contributor that increases unique intergenic sequences in a region of DNA Reverse transcriptase: enzyme copies RNA into double-stranded DNA referred to as copy DNA or cDNA miRNAS: microRNAs that are likely to be functions of unique intergenic regions in eukaryotic cells that are not yet understood Reverse transcriptase: the process in cells by which an enzyme makes a copy of DNA from RNA; makes DNA copy; catalyzes the formation of DNA copy from an RNA template in reverse transcription Microsatellite DNA: composed of very short tandemly repeated sequences and these repeats arise from difficulties in accurately duplicating the DNA which are represented nearly in 3% of human genome Genome-wide repeats: much larger than microsatellite DNA; usually found either as a single copy dispersed throughout the genome or closely spaced clusters; the common features that are classes of repeats is transposable elements Transposable elements: sequences that can move from one place in genome to another; during transposition (movement called) the element moves to a new position in the genome often leaving the original copy behind. They multiply and accumulate throughout the genome

Important Ideas:

        





Packaging DNA into chromosomes is an important function which occurs in both prokaryotic and eukaryotic organisms Completely naked DNA is relatively unstable because of its highly negative charge; in contrast, chromosomal DNA is extremely stable DNA packaging into a chromosome can be transmitted efficiently to both daughter cells when a cell divide In eukaryotic, half of its molecular mass is protein There are two proteins available in eukaryotic: histones (majority of proteins) and nonhistones Another important function of protein: compacting the DNA In human cell, DNA is compacted by many orders of magnitude to fit in a small space which are helped by histones in a process called nucleosomes Prokaryotic organisms such as bacteria has no histones or nucleosomes but have other proteins that serve a similar function as nucleosomes Traditional View: Prokaryotic cells have single circular chromosomes while eukaryotic has multiple linear chromosomes. Views have been challenged as it is possible to have both circular and linear in eukaryotic and prokaryotic cells Difficulties of Circular chromosome: require enzyme called topoisomerases to separate the daughter molecules after they are replicated. Without the enzymes, daughter cells remain interlocked with each other after replication Difficulties of linear chromosome: They have to be protected from enzymes that normally degrade DNA ends and present difficulties during DNA replication

Every Cell Maintains a Characteristic Number of Chromosome  Prokaryotic has one complete copy of their chromosome packaged into a structure called nucleoid  Unlike chromosomal DNA, plasmids are often present in many complete copies per cell  Polyploid cells have more than 2 copies of each chromosomes; some organisms have thousands of copies of each chromosomes which allows cell to generate large amounts of RNA and in turn protein  Genome size is related to the complexity of the organism; number of genes rather than genome size is more closely related to organism complexity  Organisms complexity is proportional to amount of gene present which is also called the gene density  Number of genes included in 65-kb region decreases as organism complexity increases: Ecoli has 57 genes whereas human has 2 genes. Humans therefore is more complex than Ecoli bacteria as it has less genes present More Complex Organisms have decreased Gene Density  The less complex the organism, the higher its gene density  Example: the gene density of E-coli is higher than humans as gene density of more complex organism is lower than gene density of less complex organism (E-coli)  Gene density is lower in eukaryotic than prokaryotic as eukaryotic has more complex organisms  Genes make up only a small proportion of the Eukaryotic chromosomal DNA

 2 factors that contribute to decrease gene density in eukaryotic: increase in gene size and increase inn DNA between genes also called intergenic sequences  Major reason the gene size is larger in more complex organisms (humans) is because of it has discontinuous protein-coding regions called introns which are removed from RNA after transcription in a process called RNA splicing  95% of human gene is introns and only 5% genes are protein-encoding gene that directly encodes the desired protein  Simple eukaryotic cell has fewer introns -

Regulatory Sequences is one of the contributor that increases unique intergenic sequences in a region of DNA

2 Kinds of Intergenic DNA are unique and repeated

¼ or 25% is unique

60% of human genome is composed of Intergenic DNA

-

As organisms becomes more complex and encodes for more genes, regulatory sequences grows in size and complexity to coordinate more gene expession Unique regions = includes many nonfunctional mutant genes, gene fragments and pseudogenes Mutant Genes arise from simple random mutagenesis or mistakes in DNA recombination

-

-

-

-

-

Pseudogenes arise from the action of enzyme called reverse transcriptase Small structural RNAs (miRNAs) act to regulate the expression of other genes by altering either the stability of the product mRNA or its ability to be translated Pseudogenes: It arises from the integration of reverse-transcribed messenger RNAs, they do not have introns and lack a promotor sequence Majority of human intergenic sequences are composed of Repetitive DNA 2 General classes of repeated DNA: microsatellite DNA and genome-wide repeats Microsatellite DNA is composed of very short tandemly repeated sequences and these repeats arise from difficulties in accurately duplicating the DNA which are represented nearly in 3% of human genome Genome-wide repeats: much larger than microsatellite DNA; usually found either as a single copy dispersed throughout the genome or closely spaced clusters; the common features that are classes of repeats is transposable elements Transposable elements: sequences that can move from one place in genome to another; during transposition (movement called) the element moves to a new position in the genome often leaving the original copy behind. They multiply and accumulate throughout the genome Movement of transposable elements is relatively rare in human cells but long periods of evolutionary time has made the movement possible Same features of intergenic sequence found in human genome is possible in other organism but in these organisms there is lower chance of success due to a combination of factors like inefficient duplication and more efficient elimination ` Repeated DNA = Junk DNA Intergenic DNA confers a positive value (or selective advantage) to the host organism...