Notes for Exam 2 Review Lecture 10 Bacterial Genomes Central Dogma Transcription 1 Genome entire genetic component in the cell includes genes and intervening sequences in DNA chromosome and plasmids a Chromosomes the genetic sequence that makes a species a species i Bacterial chromosomes are circular linear and lack histones ii Archaea chromosomes are circular and have histones iii Eukaryotic chromosomes are linear and have histones iv Chromosomes are usually very large so they must be compacted so they can fit into the prokaryotic cell or the eukaryotic nucleus supercoiling 1 Bacterial chromosome is supercoiled into star like wheels 2 Eukaryotic chromosomes are supercoiled by forming nucleosomes eight histones b Plasmids independently replicating circular DNA structures that can be passed between cells through horizontal gene transfer regulate their own copy number i Bacteria usually have more than one plasmid ii Archaea can have plasmids iii Eukaryotic protozoa and fungi can have plasmids c Genome has genes that encode proteins regulatory sequences like promoters or protein binding domains think of the lac operon structure i Bacteria Archaea circular linear dsDNA in bacteria and circular dsDNA in archaea in nucleoid in cytosol ii Eukaryotes linear dsDNA in nucleus also have mitochondrial and chloroplast DNA in the mitochondria and chloroplasts remember endosymbiosis theory d Replicon molecule that contains all the genes needed to duplicate itself chromosome plasmid e The number of genome copies denotes ploidy haploid organisms have one copy of their genome diploid organisms have two copies of their genomes tetraploid organisms have four copies of their genomes etc i Haploid Bacteria have single copy of each gene in chromosome therefore a mutation has the potential for an immediate effect on phenotype of the bacterium because there is no second allele to mask the change 1 Archaea are also haploid 2 For example E coli has a single copy of lacZ gene During a replication the DNA polymerase introduces a deleterious mutation that makes LacZ nonfunctional That cell thus immediately can no longer use lactose as a carbon source It went from a lac E coli that could grow on lactose minimal media to a lac E coli that can t grow on lactose minimal media Here a genotypic change most likely causes an observable phenotypic change ii Diploid Higher eukaryotes like humans have 2 alleles dominant recessive genotypes mask mutant phenotypes So being diploid is a bit of insurance to protect the organism against deleterious alleles if you have one bad allele and one good allele the good allele will compensate for the bad one thus you hopefully will be okay and not show disease Bacteria are diploid only during cell division and replication of the chromosome 1 For example Tay Sachs disease in humans is a genetic disorder where nerve cells progressively deteriorate It is caused by mutations in the HEXA gene two Tay Sachs HEXA alleles must be inherited to see disease Therefore a human can have one Tay Sachs allele and one normal allele at the HEXA locus and not have disease because the normal allele compensates for the Tay Sachs allele Here the normal allele is masking the Tay Sachs allele so we do not get an observable phenotypic change 2 Genotype the actual sequence of the DNA encoding genes in the genome If two organisms have the same genotype they are considered genetically identical or isogenic iso equal or same genic gene 3 Phenotype the observable properties or functions of an organism includes shape motility metabolism growth virulence etc 4 Three types of genetic information flow vertical and horizontal a Within a cell Central Dogma DNA to RNA to protein a gene in DNA is transcribed to mRNA which is then translated to protein i Gene names are italicized while protein names are not b Vertical gene transfer from parent to offspring you are going down the generation c Horizontal gene transfer between organisms of the same generation you are going tree across on the generation tree 5 Central Dogma DNA to RNA to Protein a DNA structure i Chains of four nucleotides A adenine T thymine G guanine C cytosine 1 A forms two hydrogen bonds with T G forms three hydrogen bonds with C A T and G C are complementary base pairs one always binds with the other 2 These hydrogen bonds bind two strands of DNA together into a double helix 3 Base 3 phosphates base name triphosphate deoxyribonucleotide dNTP when N is replaced by either A T C or G 4 Base one phosphate base name nucleotide dNMP ii DNA has 5 and 3 polarity synthesized from 5 to 3 1 Two strands run anti parallel to each other one strand runs 5 3 and the other runs 3 5 2 Sense strand runs 5 3 while antisense strand runs 3 5 iii DNA is double stranded most of the time unless it is at a replication fork where it has been unzipped by helicase but the complementary strand has not yet been synthesized by DNA polymerase b RNA also has 5 and 3 polarity RNA is single stranded most of the time i RNA is synthesized 5 3 from DNA template strand transcription c Proteins have N termini and C termini i Proteins are synthesized N terminus to C terminus by ribosome translation 6 DNA Replication a Pictures and videos are your friend here MAKE SURE YOU CAN DRAW A REPLICATION b Parent cell genome must be replicated before division replication begins at origins of c Parent cell genome is template DNA directional DNA synthesis 5 3 d Prokaryotes have bidirectional synthesis have two replication machines at each fork of a replication bubble going in opposite direction BOTH NEW STRANDS ARE STILL MADE 5 3 CANNOT HAVE 3 5 SYNTHESIS EVER e Replication is semiconservative made of one old strand and one newly synthesized FORK replication strand f New strand needs to be methylated after replication g Needs many proteins to do different jobs enzyme mediated i Helicase unzips helix of DNA exposing both strands to the rest of the DNA replication machinery makes dsDNA into ssDNA creates the replication bubble with a leading and lagging strand at each fork ssDNA is bound by stabilizing proteins single stranded DNA binding proteins ii iii Primase makes RNA primers on the single strands because DNA polymerase DNAP needs a RNA primer to begin synthesizing DNA iv Leading strand will be continuously synthesized 5 3 by DNA polymerase which incorporates dNTPs into the growing strand the DNAP is moving in the same direction as the replication fork v Lagging strand has to be synthesized in Okazaki