BIOL 1108 - CH 13 - Genomes PDF

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This set of notes includes information on genome sequencing, genome annotation, HIV genomes, how bacterial cells package their DNA as a nucleoid composed of many loops, the 22 pairs of the human genome and more. Teacher: Ricardo Fiorillo...

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CH 13 - Genomes Tuesday, December 6, 2016

3:10 PM

Genome Sequencing (PG 272)

- Genome ○ Refers to the genetic material of a specified organism, cell, nucleus, organelle, or virus - The human genome ○ Refers to the DNA in the chromosomes present in a reproductive cell, like an egg or sperm ○ Human genome = 23 - The genome sequence is a string of A's, T's, G's and C's Complete Genome Sequences are Assembled From Smaller Pieces (PG 272) 1. Obtain short stretches of the genome 2. Sequence assembly - The short sequences are put together in the correct order to generate the long, continuous sequence of nucleotides in the DNA molecule present in each chromosome a. The short sequences are assembled according to their overlaps

- Shotgun Sequencing - Short sequences are assembled according to their overlaps (Like above) ○ The sequenced fragments don't originate from a particular gene or region but from sites scattered randomly across the chromosome

Sequences that are repeated complicate sequence assembly (PG 273) -

overlaps between fragments must be long enough to ensure that the assembly is correct and to determine from which strand of DNA the short sequence is obtained

- Challenges and Limitations ○ Repetitive DNA (repeated sequences) ▪ Long repeated sequences are usually much longer than the short fragments and the repeat may not be detected at all. If the repeat is detected, there is no easy way of knowing the number of copies of the repeat (whether the DNA molecule includes, 2, 3, 4 or any number of copies of the repeat). ▪ Sometimes the ends can be used

What sequences your personal genome? (PG 274) - There is really no such thing as the Human Genome - Every person's genome is unique with the exception of identical twins - The human genome is a composite of sequences from different individuals - Personalized Medicine - an individual's genome sequence, by revealing his or her disease susceptibilities and drug sensitivities, allows treatments to be tailored to that person

Genome Annotation (PG 275) - Goal of Biology: To identify all the macromolecules in biological systems and understand their individual functions and ways in which they interact - Genome sequence contains in coded form, the nucleotide sequence of all RNA molecules transcribed from the DNA as well as the amino acid sequence of all proteins

- A genome sequence is merely an extremely long list of A's, T's, G's and C's that represent the order in which nucleotides occur along the DNA in one strand of the double helix - Not all DNA is transcribed into RNA and not all RNA is translated into protein

Genome annotation identifies various types of sequence (PG 275)

- Noncoding RNAs - are sequences that are not translated into protein such as ribosomal RNA, transfer RNA - Genome Annotation - is the process by which researchers identify the various types of sequence present in genomes. ○ An exercise in adding commentary to a genome sequence that identifies which types of sequence are present and where they are located - A sequence that is annotated as nonfunctional today may be found to have a function tomorrow

Genome annotation includes searching for sequence motifs (PG 276) - Genome annotation begins with the identification of patterns called Sequence Motifs, telltale sequences of nucleotides that indicate what types of function ( or absence of function) may be encoded in a particular region of the genome - Sequence Motifs can be found in the DNA itself or in the RNA sequence inferred from the DNA sequence ○ Example: Promoter - is a sequence where RNA polymerase and associated proteins bind to the DNA to initiate transcription ○ Example: Open Reading Frame (ORF) a long string of nucleotides that, if transcribed and processed into messenger RNA would result in a set of codons for amino acid that does not contain a stop codon. ▪ Putative ORF doesn't necessarily code for protein. They may not be transcribed, if it is transcribed, it might be in a noncoding RNA or an intron of a protein-coding RNA

Comparison of Genomic DNA with messenger RNA reveals the intron-exon structure of genes (PG 276)

An annotated genome summarizes knowledge, guides research, and reveals evolutionary relationships among organisms (PG 277) - Genome annotation aims to identify all the functional and repeat sequences present in the genome - Genome sequences contain information about ancestry and evolution ○ Comparisons among genomes can reveal how different species are related ○ The human genome is more similar to a chimpanzee than to a gorilla

- Comparative Genomics help us to understand how genes and genomes evolve - Conserved are sequences that are similar in different organisms ○ Likely to be very important

The HIV genome illustrates the utility of genome annotation and comparison (PG 277) - Virus is a small infectious agent that contains a nucleic acid genome packaged inside a protein coat called a Capsid ○ Use cellular ATP and hijack cellular machinery to replicate, transcribe, and translate their genome in order to make more viruses ○ The genome of HIV is single-stranded RNA ▪ It is a retrovirus that replicates by a DNA intermediate that can be incorporated into the host genome

- The evolutionary tree shows that closely related viruses have closely related hosts

- Gag encodes protein components of the capsid - Pol encodes proteins needed for reverse transcription of the viral RNA into DNA and incorporation into the host genome - Env encodes proteins that are embedded in the lipid envelope

Viruses, bacteria, and archaeons have small, compact genomes (PG 279)

- Genomes are measured in numbers of base pairs, and the yardsticks of genome size are a thousand base pairs (a kilobase, Gb), a million base pairs (a megabase, Mb) and a billion base pairs (a gigabase, Gb) - The largest viral genome is the amoeba Acanthamoeba Polyphaga (1.2 Mb) - Bacterial genomes range in size from 0.5 to 10 Mb ○ Bigger genomes nave more genes, allowing these bacterial to synthesize small molecules that other bacteria have to scrounge for, or to use chemical energy in the covalent bonds of substances that other bacteria cannot

- C-Value Paradox - The disconnect between genome size and organismal complexity ○ It is the amount of DNA in a reproductive cell and the paradox is the apparent contradiction between genome size and organismal complexity, leading to the difficulty of predicting one from the other - Why some eukaryotic genomes are so large ○ Polyploidy, or having more than two sets of chromosomes in the genome - Humans have 2 sets of 23 chromosomes, giving us 46 in total - Polyploidy has played an important role in plant evolution ○ Polyploidy plants include: Wheat, potatoes, olives, bananas, sugarcane, and coffee

About half of the human genome consists of transposable elements and other types of repetitive DNA (PG 280)

- In the human genome only about 2.5% of the genome actually codes for proteins ○ The other 97.5% includes sequences including introns, noncoding DNA, and various types of repetitive sequences - Among the repeated sequences is alpha α satellite DNA which consists of tandem copies of 171-bp sequence repeated near each centromere an average of 18,000 times ○ The α satellite DNS is essential for attachment of spindle fibers to the centromeres during cell division

- Transposable Elements (repeated sequence), also called Transposons which are DNA sequences that can replicate and insert themselves into new positions in the genome ○ Have the potential to increase their copy potential over time ○ Sometimes referred to as "Selfish" DNA because it seems that their only function is to duplicate themselves and proliferate in the genome making them the ultimate parasite ○ Make up about 45% of the DNA in the human genome ○ Can be grouped into 2 classes: ▪ DNA Transposons which replicate and transpose by DNA replication and repair ▪ Retrotransposons which consists of elements that transpose by means of an RNA intermediate □ Their RNA is used as a template to synthesize complementary strands of DNA, a process that reverses the usual flow of genetic information from DNA into RNA (retro- means backwards)

□ More than 40% of the human genome consists of various types of retrotransposons

Bacterial cells package their DNA as a nucleoid composed of many loops (PG 281) - Bacterial genomes are circular ○ The DNA helix is underwound ○ Underwinding is caused by Topoisomerase II, which breaks the double helix, rotates the ends to unwind the helix, and then seals the break.

- Underwinding causes stress on the DNA which is relieved by the formation of Supercoils, in which the DNA molecule coils on itself ○ Supercoiling allows all the base pairs to form, even though the molecule is underwound ○ Supercoils that result from underwinding are called Negative Supercoils (Most DNA) ○ Supercoils that result from overwinding are called Positive Supercoils - In bacteria, the supercoils of DNA form a structure with multiple loops called a Nucleoid which has about 100 loops, each with 50 kb of DNA

Eukaryotic cells package their DNA as one molecule per chromosome (PG 282) - Eukaryotic DNA is linear and each DNA molecule forms a single chromosome - Chromatin DNA is packaged with protein to form a DNA complex ○ Levels of Packaging: ▪ First, eukaryotic DNA is wrapped twice around a group of histone proteins called Nucleosome □ A nucleosome is made up of 8 histone proteins: 2 each of histones H2A, H2B, H3 and H4 which are rich in the amino acids lysine, and arginine whose positive charges are attracted to the negative charges of the phosphates along the backbone of each DNA strand □ First level is sometimes referred to as "Beads on a String" (Nucleosomes = the beads, and DNA = the string) ▪ Second, occurs when the chromatin is more tightly coiled forming a 30-nm fiber □ Progressive packaging constitute Chromosome Condensation, an active, energy-consuming process requiring the participation of several types of proteins

The Human Genome Consists of 22 Pairs of Chromosomes and Two Sex Chromosomes (PG 282) - Chromosome pairs usually match in size, general appearance, and position of the centromere, but there are exceptions, such as the X and Y chromosomes - Homologous Chromosomes are pairs of chromosomes that match in size and appearance ○ Have the same genes arranged in the same order along their length ○ If the DNA duplexes in each pair of homologs were denatured, each DNA strand could forma duplex with its complementary strand from the other homolog - Metaphase in mitosis is the easiest stage in which to isolate chromosomes because of the availability of chemicals that prevent the spindle form forming ○ Under fluorescent light, dyes give the DNA in each type of chromosome a different color ○ Two members of each pair of homologous chromosomes show the same pattern of fluorescent color - Standard form of chromosomes = Karyotype where the chromosomes are arranged in pairs from longest to shortest with the sex chromosomes placed at the lower right ○ Male = X and Y ○ Female = 2 X's ○ Humans have 23 pairs of chromosomes

- Giemsa Stains yield about 300 bands that are used as landmarks for describing the location of genes along the chromosomes

- Chromosomes come in pairs except for sex chromosomes and polyploids ○ The occurrence of chromosomes in pairs allows eukaryotes to reproduce sexually

Organelle DNA forms nucleoids that differ from those in bacteria (PG 285)

- Most eukaryotic cells contain mitochondria and many contain chloroplasts ○ Each one has a Nuclear Genome consisting of the DNA in the chromosomes ○ Cells with mitochondria also have a Mitochondrial Genome ○ Cells with a chloroplast also have a Chloroplast Genome - Most biologist subscribe to the theory that the organelles originated as free-living bacterial cells that were engulfed by primitive eukaryotic cells billions of years ago - DNA is mitochondria and chloroplasts is usually circular and exists in multiple copies per organelle - Plant chloroplast DNA is more uniform in size than mitochondrial DNA

Viruses and Viral Genomes (PG 285)

- Viral genomes are small and compact with little or no repetitive DNA ○ Very diverse ○ Classified based on their type of genome and mode of replication - Some viruses transfer genetic material from one cell to another in a process called Horizontal Gene Transfer to distinguish it from parent-to-offspring (vertical) gene transfer which plays a major role in the evolution of bacterial and archaeal genomes as well as in the origin and spread of antibiotic-resistance genes - Viruses can only reproduce by hijacking host-cell functions, but as a group they have had great evolutionary success

Viruses can be classified by their genome (PG 286) - The T4 virus infects cells of the bacterium Escherichia Coli - Bacteriophages are viruses that infect bacterial cells - The adenovirus is a common cause of upper respiratory infections in humans ○ This type of virus is surrounded by a glycoprotein envelope composed of a lipid bilayer embedded with proteins

Viruses are capable of self-assembly (PG 288)

- The genome of a virus contains the genetic information needed to specify all the structural components...