Module 03 - Section 06 Flashcards
Genome Formatting and Structure
What is the genome?
Complete set of genetic material encoded in a cell or virus.
For many sexually reproducing organisms, the genome includes one set of autosomes and two sex chromosomes
Contain both coding and non-coding information
Is the DNA contained in organelles part of the genome?
no
Do viruses have genomes?
yes, but theirs is defined as the complete copy of the nucleic acid required to specify the virus, as they contain both DNA and RNA as genetic material
What is a gene?
A chromosomal segment that codes for a single functional polypeptide chain or RNA molecule
What are the 2 main components of the genome?
(1) Functional DNA
(2) Non-Functional DNA
What is functional DNA?
Functional DNA improves an organism’s fitness, and therefore these functional components are highly conserved (sequence-wise)
What is non-functional DNA?
It has no known biological contibutions
Do these genomes contain mostly functional or non-functional DNA?
(a) Prokaryote
(b) Eukaryote
(a) Functional
(b) non-functional
What is the 2 types of functional DNA?
(1) Coding DNA
(2) Non Coding DNA
What is coding DNA?
Codes for a specific protein
What is non coding DNA?
Does not code for a protein, but still has an important role, like regulation of gene expression or contributing to genomic complexity and/or variation
What does the human genome consist of? (3 characteristics)
(1) approx 3 billion nucleotide BPs
(2) 23 pairs of chromosome (22 autosomes and 2 sex chromosomes)
(3) estimated 20,000 to 25,000 genes
What is the human genome project?
Project initiated in 1990 that set out to sequence all of the genes in the human genome. It was completed in 2003
Describe the genome of bacteria
Their genome consists of a single circular DNA molecule several million base pairs long - genome of at least 1 species from virtually every known bacterial family has been sequenced
What are archea?
unicellular organisms with no internal organelles of nucleus. While they are similar to bacteria, they are more closely related to eukaryotes with respect to some genes and metabolic pathways
Why are archea important targets for study and genome sequencing
Their contributions to the chemistry of the biosphere as they include many species that thrive in extreme environments of high ionic strength, high temperature or low pH
What archaebacterium is used in molecular biology for isolating a heat resistant Taq Pol for PCR?
Streptococcus mutans
Describe the eukaryotic genome
Often considerably larger than genomes of bacteria or archae, consisting of billions of nucleotides
What are orthologs?
Genes from different species that evolved from a common ancestor - 2 genes in different species possess a clear sequence and functional relationship
What is LUCA?
Last Universal Common Ancestor and it he single-celled organism that gave right to all life on earth
Describe the structure of chromosomes (3 characteristics)
(1) Shorter P-arm
(2) Longer Q-arm
(3) Centromere that separates the P-arm from the Q-arm
How many chromosomes are in genomic human DNA?
46
22 homologous pairs of autosomes (44)
2 sex chromosomes (female = XX and male = XY)
How many base pairs are there per chromosomes?
from 50 to 250 MILLION base pairs of DNA
What is the dye Giemsa used for?
It tells us which areas are being actively expressed
dark = heterochromatin, not being expressed
light = euchromatin, actively expressed
What is heterochromatin?
Condensed portion of chromosomes that are not transcriptionally active
What is Euchromatin?
Areas of chromosome in which the genes are being actively expressed
What are the 2 closest relatives to humans according to their genome
(1) chimpanzee
(2) bonobo
What are the two types of genomic differences found between humans and chimpanzees
(1) Single nucleotide polymorphisms (SNPs)
(2) Large genomic rearrangements
What are Single nucleotide polymorphisms? (SNPs)
Represent a genomic base pair change that helps distinguish one species from another, or one subset of individuals in a population
– Most common type of genetic variance among different people
What are large genomic rearrangements?
Refer to larger alterations within the DNA sequence of chromosomes
What are the 2 kinds of genomic rearrangements?
(1) Inversions
(2) Fusions
What are inversions in genomic rearrangement?
Refer to a mutation that results from the inversion of a large segment of DNA in a chromosome
– caused by segmental duplication, transporition of one copy to another arm of the same chromosome, and recombination between the 2 segments
What are fusions in genomic rearrangement?
Refer to the rearrangement of chromosomal DNA by deletion, duplication, insertion, or transposition to form a hybrid gene
On which chromosome can you find inversions in the human lineage?
1, 12, 15, 16, and 18
What is a genomic locus?
A particular position in a chromosome
What are outgroups in genomic comparison?
More distantly related organisms
What are homologs?
Any 2 genes with a demonstrable sequence similarity, whether or not they are closely related by function. The sequence similarity implies an evolutionary relationship – sequence similarity and a functional relationship go hand-in-hand
What are paralogs?
Genes that are similarly related to each other but within a single species. Most often arise from gene duplication in a single genome, followed by specialization of one or both copies of the gene over the course of evolution
Give an example of paralogs
In mice, there is the insulin 1 (Ins1) and insulin 2 (Ins2) genes, both of which encode for the hormone insulin
Give an example of orthologs
Leptin (hormone involved in regulation of appetite) both humans (LEP) and mice (lep) have the gene for leptin and it plays a similar role in both
What are the 8 necessary components within a genome?
(1) Coding sequences for RNA and protein molecules
(2) Signals for chromatin condensation/chromating remodeling
(3) Signals for initiation of replication and chromosomal integrity
(4) Control signal for on/off levels of expression
(5) Start and stop sites for transcription
(6) Processing signals for primary transcripts
(7) Control signals for dynamic access at right time and place
(8) Identifiers for coding sequences that must be coordinately or sequentially expressed
What is the proportion of coding or exonic DNA vs the entire genome
less than 1.5%
What are the 3 components of a single gene?
(1) Promoter sequence
(2) exons
(3) introns
What is splicing?
Process of removing introns from a primary RNA transcript
How can one gene have multiple protein products?
alternative splicing
What does an exon often encode for?
a single domain of a larger, multidomain protein
What is a pseudogene?
A section of a chromosome that is an imperfect copy of a functional gene
What does the phrase “evolution seems to prefer splitting of genes” mean?
In genes highly conserved across all organisms, more complex organisms have introns while simpler organisms do not
Why do humans and other vertebrates use RNA splicing extensively while simple organisms do not?
Alternative splicing allows multiple, functionally distinct proteins to be encoded by a single gene. This increases protein diversity. Splicing can be specific to certain tissues, conditions, and developmental states
