[2S] UNIT 4 Genomes and Variant Flashcards
Study of totality of genome of a living organism
Genomics
Total nucleic acid sequences and what will it be translated into a living organism, including viruses
Genome
the coding material; distinct sequence of
nucleotides, forming part of a chromosome
Genes
Compact bacterial chromosome
Nucleoid
About a third of the volume of the cell
Bacterial genomes
- supercoil loop of DNA
- randomly distributed
chromosomal domains
T/F: Bacterial chromosomes are majority circular and some are linear
T
Multiple 1-Mb chromosomes
Borrelia spp.
8-Mb chromosomes
Streptomyces spp.
T/F: In prokaryotic cells, since there are no membrane-bound organelles (ex. nucleus and mitochondria), the genome is packaged into a nucleoid
T
_____ with DNA bridging, wrapping, or bending activities contribute to the organization of the chromosome
Nucleoid-associated proteins (NAPs)
T/F: Viruses are composed of both RNA or DNA
F; Viruses are composed of either RNA or DNA (never both)
VIRAL GENOME
Nucleic acid genome
RNA or DNA (never both)
VIRAL GENOME
symmetrical or quasi symmetrical
capsid
VIRAL GENOME
a protein that encodes the nucleic acid (DNA / RNA)
capsid
virus that infects bacteria and archaea
bacteriophage
bacteriophage greek term meaning
bacteria eater
how many base pairs are in a human genome?
3.4 billion base pairs
a type of packaging for complex viruses wherein the viral capsid is constructed first, then the genetic material enters
Phage lambda maturation
average gene of a human genome
3000 bases, vary in size
Largest known human gene ______ at 2.4M bases
dystrophin
T/F: Almost all (99.9%) nucleotide bases are exactly the same in all people.
T
HUMAN GENOME
T/F: Unknown function: 50% of discovered genes
T
T/F: The more complex the cell gets, their genetic material becomes shorter but it does not necessarily mean that they contain more functional units
F; longer
DNA packaging and the various packing capacities involved to fit eukaryotic DNA into the nucleus
Nucleosome structure
The process of phage lambda maturation begins with a change in the shape of the _____ head, which fills with DNA and expands.
empty
Counterpart of histones in eukaryotes
Nucleoid-associated proteins (NAPs)
CORE HISTONE VARIANTS IN VERTEBRATE DEVT.
Number of Gene Copies: 2
Cell Cycle Exp: RI
Loc: Throughout the genome
Function: Gene activation and silencing
Knockout Pheno: Embryonic infertility
H2A.Z
CORE HISTONE VARIANTS IN VERTEBRATE DEVT.
Number of Gene Copies: 15
Cell Cycle Exp: RD
Function: Core Histone
Knockout Pheno: Not determined
H2A
CORE HISTONE VARIANTS IN VERTEBRATE DEVT.
Number of Gene Copies: 1
Cell Cycle Exp: RI
Loc: Throughout the genome
Function: DNA repair
Knockout Pheno: Sperm defect in meiosis
H2A.X
CORE HISTONE VARIANTS IN HUMAN DISEASE
No. of Gene Copies: 1
Cell Cycle Exp: RI
Mutation & Exp Patterns: Reduced expression
Tumor Conseq: Inc cancer progression in p53 KO mice
H2A.X
CORE HISTONE VARIANTS IN HUMAN DISEASE
No. of Gene Copies: 2
Cell Cycle Exp: RI
Mutation & Exp Patterns: Over progression (oncogene)
Tumor Conseq: Numerous cancers
H2A.Z
CORE HISTONE VARIANTS IN HUMAN DISEASE
No. of Gene Copies: 2
Cell Cycle Exp: Possibly RI
Mutation & Exp Patterns: Reduced expression (tumor sup.)
Tumor Conseq: Melanomas and numerous cancers
MacroH2A
CORE HISTONE VARIANTS IN HUMAN DISEASE
No. of Gene Copies: 10
Cell Cycle Exp: RD
Mutation & Exp Patterns: K27M in H3
Tumor Conseq: Adult and pediatric glomas, including GBMs
H3.1
LAMPBRUSH CHROMOSOME
Appear at the meiosis stage in which the chromosomes resemble a series of beads on a string
Chromomeres
Lateral loops that extrude from the chromomeres at certain positions.
Lampbrush chromosome
LAMPBRUSH CHROMOSOME
Extruded segment of DNA actively transcribed
Loop
LAMPBRUSH CHROMOSOME
Urodele amphibians
Oocytes
Diplotene prophase chromosomes
Lampbrush chromosome
Usually found at the interphase nuclei of some tissue of the larvae of flies
Polytene Chromosome
Useful for the analysis of many facets of eukaryotic interphase chromosome organization and the genome as a whole
Polytene Chromosome
Develop from the chromosomes of diploid nuclei by successive duplication of each chromosomal element (chromatid)
Polytene Chromosome
Cells with polytene chromosomes differ in many ways from mitotically dividing cells
Polytene Chromosome
T/F: Genome size is not necessarily related to the gene number in EUKARYOTES
T
a primer set has a target locus
Pathogenicity islands
THE FEATURES OF GENOMIC SEQUENCES
Has nonrepetitive DNA
Prokaryotes
have pathogenicity islands, which are DNA segments (10-200 kb) present in genomes of pathogenic species but are absent in genomes of nonpathogenic variants of the same species
Pathogenic bacteria
THE FEATURES OF GENOMIC SEQUENCES
Moderately Repetitive & Highly Repetitive Sequences
Repetitive DNA
THE FEATURES OF GENOMIC SEQUENCES
Repetitive Transposed Sequences
MODERATELY REPETITIVE DNA: Interspered Elements
THE FEATURES OF GENOMIC SEQUENCES
VNTRs and STRs
MODERATELY REPETITIVE DNA: Tandem Repeated DNA
Sequences that are unique: only one copy in a haploid genome
Nonrepetitive DNA
T/F: Length of the nonrepetitive DNA decrease with overall genome size
F; increase
Usually corresponds to the protein coding genes
Nonrepetitive DNA
T/F: In nonrepetitive DNA, the increase in genome size for higher eukaryotes, usually reflects the increase in the amount and proportion of repetitive DNA
T
THE FEATURES OF GENOMIC SEQUENCES
One copy in a haploid genome and varies widely among taxonomic groups
Nonrepetitive DNA
T/F: Variation in genome size results from the differences in the amount of repetitive DNA, and therefore the relationship between genome size and gene number is stronger in eukaryotic genomes than in prokaryotic genomes
F; weaker
THE FEATURES OF GENOMIC SEQUENCES
DNA that do not carry critical information
Repetitive DNA
THE FEATURES OF GENOMIC SEQUENCES
Genomes of plants and amphibian, 80% of the genome
Repetitive DNA
THE FEATURES OF GENOMIC SEQUENCES
The amount of DNA in the unreplicated genome, or the haploid genome, of a species is known as the?
C-value or Constant value
THE FEATURES OF GENOMIC SEQUENCES
T/F: Unicellular eukaryotes, most of the DNA is nonrepetitive and only 20% of the genomic sequences are repetitive DNA
T
INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES
Short sequences of DNA
Transposons / Selfish or Junk DNA
INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES
Ability to move to new locations in the genome
Transposons / Selfish or Junk DNA
INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES
Propagate without contributing to the development and functioning of the organism
Transposons / Selfish or Junk DNA
INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES
<500 base pairs long and may be present 500,000 times or more in a human genome
SINEs (Short interspersed elements)
INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES
■ 200 to 300 base pairs long
■ Are dispersed uniformly throughout
the genome
SINEs: Alu family
INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES
Potential for transposition within the genome related to chromosome rearrangements during evolution
SINEs: Alu family
INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES
About 6kb in length and may be present
850,000 times in the human genome
LINEs (long interspersed elements)
INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES
Retrotransposons
LINEs (long interspersed elements)
INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES
Function as retrotransposons in retroviruses. For humans, the function is unknown
LINEs (long interspersed elements)
INTERSPERSED ELEMENTS – REPETITIVE TRANSPOSED SEQUENCES
Jumping genes
Transposons
TANDEM REPEATED DNA – VNTRs and STRs
with 2- to 5-bp repeats and an array size on the order of 10-100 units
Microsatellites
TANDEM REPEATED DNA – VNTRs and STRs
Di-, tri-, tetra-, and pentanucleotides
Short Tandem Repeats (STRs)
TANDEM REPEATED DNA – VNTRs and STRs
Dispersed throughout the genome
and vary among individuals in the number of repeats present at any site
Short Tandem Repeats (STRs)
TANDEM REPEATED DNA – VNTRs and STRs
Useful for establishing lineages or blood relations
Short Tandem Repeats (STRs)
TANDEM REPEATED DNA – VNTRs and STRs
Used in forensic DNA profiling to identify missing persons, confirmation of blood relations, and link persons of interest to suspect a crime
Short Tandem Repeats (STRs)
TANDEM REPEATED DNA – VNTRs and STRs
with 10- to 100-bp (usually around 15-bp) repeats and an array size of 0.5-30 kb
Minisatellites
TANDEM REPEATED DNA – VNTRs and STRs
■ 15 to 100 bp long
■ Found within and between genes
Variable Number Tandem Repeats (VNTRs)
TANDEM REPEATED DNA – VNTRs and STRs
Number of tandem copies of each specific sequence at each location varies from one individual to the next
Variable Number Tandem Repeats (VNTRs)
TANDEM REPEATED DNA – VNTRs and STRs
Variation in size between individual humans is the basis for DNA fingerprinting
Variable Number Tandem Repeats (VNTRs)
HIGHLY REPETITIVE SEQUENCES
● Highly repetitive DNA
● Short sequences repeated a large number of times
Satellite DNA (satDNA)
HIGHLY REPETITIVE SEQUENCES
Variable AT-rich repeat forms arrays up to 100Mb
Satellite DNA (satDNA)
HIGHLY REPETITIVE SEQUENCES
Satellite monomer length
150 to 400bp
HIGHLY REPETITIVE SEQUENCES
satDNA location
Heterochromatic regions (mostly centromeric & subtelomeric but also intercalary posi)
HIGHLY REPETITIVE SEQUENCES
Are likely involved in sequence-specific interactions and subsequently in epigenetic processes
Satellite DNA (satDNA)
NONCODING SEQUENCES
Appear to turn over rapidly, but can be strongly influenced by positive selection
MicroRNAs
HIGHLY REPETITIVE SEQUENCES
Has a sequence-independent role in the formation and maintenance of heterochromatin
Satellite DNA (satDNA)
HIGHLY REPETITIVE SEQUENCES
Transcripts produce siRNAs
○ Involved in posttranscriptional gene regulation through the action of the RNA-induced silencing complex (RISC)
Satellite DNA (satDNA)
NONCODING SEQUENCES
Have been found to play a important role in neuronal functions
Noncoding RNAs
NONCODING SEQUENCES
Dead genes
Pseudogenes
NONCODING SEQUENCES
○ May evolve functions in regulating expression of related genes
○ May regulate their parental genes, similar to long noncoding RNAs or microRNAs (miRNAs)
Pseudogenes
NONCODING SEQUENCES
DNA sequences representing evolutionary vestiges of duplicated copies of genes that have undergone significant mutation alteration
Pseudogenes
Alter the amino acid sequence leading to functional changes in proteins
Nonsynonymous Mutation
2 Nonsynonymous mutation
Missense codon
Nonsense codon
Silent mutation
Synonymous mutation
○ Replication error or DNA damage
○ Protein-coding region
○ Substitution mutation
Mutation
Do not change the amino acid sequence of a protein
Silent Mutation
Change 1 amino acid to another
Missense Codon
frequency at which genetic mutations accumulate over time between different populations or species
Rate of Divergence
Introduce a premature stop codon, truncating the protein
Nonsense Codon
Calculates the time of divergence between the 2 members of the family
Rate of Divergence (galing s bibig ni maam yn dk gets)
GENOME EVOLUTION
Second step
Fixation of Mutation
GENOME EVOLUTION
Over successive generations
Fixation of Mutation
GENOME EVOLUTION
Molecular change a feature of the entire phylogenetic unit such as population, species, or lineage
Fixation of Mutation
GENOME EVOLUTION
Predictable by probability (selectively neutral or near-neutral)
Fixation of Mutation
GENOME EVOLUTION
Random changes in the frequency of a mutational variant in a population
Genetic Drift
GENOME EVOLUTION
A variant may be either lost from the population or fixed, replacing all other variants.
Genetic Drift
GENOME EVOLUTION
Usually in the form of nucleotide substitutions.
Genetic Drift
GENOME EVOLUTION
A combination of the mutation rate and the rate of fixation
Evolutionary Rate
GENOME EVOLUTION
T/F: In evolutionary rate, when we compare the rate between species or genes, a portion of the difference comes from the changes in the mutation rate and a portion from the changes in the rate of fixation
T
GENOME EVOLUTION
T/F: Substitution rate is equal to the mutation rate
T
GENOME EVOLUTION
The overall influence that a life history trait has on sequence evolution rate is then largely a result of the ______ & _______ of its effects on mutation and fixation rates
magnitude and directions
GENOME EVOLUTION
_______ _____ will overcome selection to a greater extent in smaller populations, slightly deleterious mutations are more likely to become fixed in species with small effective population sizes
Genetic drift
ODD ONE OUT: Mechanisms of Genome Evolution
● Gene duplication
● De Novo Origination
● Horizontal Gene Transfer
● Gene Recombination
● New Gene Regulatory Systems
● Transposable Elements
● Molecular Evolution of Repetitive Sequences
● Evolution Rate of Repetitive DNA Sequences
● Mitochondrial Genome
Mitochondrial Genome - kinuha k lng khit san
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
Smaller genomes are favored directly by selection as a way to cellular economization
The Streamlining Hypothesis
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
Most common explanation for genome reduction in free-living bacteria
The Streamlining Hypothesis
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
Natural selection directly favors genome reduction and low G+C content in free-living prokaryotes living in low-nutrient environments
The Streamlining Hypothesis
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
Small intergenic regions and small cell size
The Streamlining Hypothesis
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
Mainly determined by the intracellular environment
The Streamlining Hypothesis
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
Genes unnecessary for living in intracellular conditions are not maintained by selection and are lost in the course of evolution
The Streamlining Hypothesis
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
In populations undergoing constant bottlenecks and no recombination, genome reduction occurs through the accumulation of slightly deleterious mutations
The Muller Ratchet
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
Selection fails to retain gene, which then, by the constant accumulation of mutations, become inactive and are eventually deleted from the genome
The Muller Ratchet
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
T/F: The Impact of Genome Reduction on Host-Associated Bacteria
- Modifications of some genes coded in the reduced genome could allow the exosymbiont to cope with the loss of otherwise essential genes;
F; endosymbiont
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
Several of the typical characteristics of these genomes, such as theri large A+T content or their small genomes, reflect known mutational biases (i.e., G:C to A:T mutations and deletions over insertions) rather than adaptations evolved by selection
The Muller Ratchet
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
T/F: The Impact of Genome Reduction on Host-Associated Bacteria
- The presence of complementary genes in the genomes of cosymbionts (if any) may compensate for gene losses in the endosymbiont
T
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
T/F: The Impact of Genome Reduction on Host-Associated Bacteria
Genes coded in the genome of the host compensate for gene losses in the genome of the endosymbiont
T
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
T/F: The Impact of Genome Reduction on Host-Associated Bacteria
- From the endosymbiont and transferred to the host
T
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
T/F: The Impact of Genome Reduction on Host-Associated Bacteria:
- Host origin
T
EVOLUTION OF THE PROKARYOTIC GENOME: GENOME REDUCTION
T/F: The Impact of Genome Reduction on Host-Associated Bacteria
- Vertically transferred from unrelated organisms not participating in the symbiosis to the host genome or its endosymbionts
F; horizontally
How many nucleotide pairs are in a mitochondrial genome?
16,569 nucleotide pairs
GENOMIC STRUCTURE
Each DNA molecule is organized into discrete units called
chromosomes
How many proteins, rRNA & tRNAs are in a mitochondrial genome?
- 13 proteins
- 2 rRNA
- 22 tRNAs.
GENOMIC STRUCTURE
The total genetic information stored in the chromosomes are referred to as the ______ of the organism.
genome
GENOMIC STRUCTURE
T/F: The human genome contains approximately 3 x 109 nucleotide base pairs packages into 23 pairs of chromosomes.
T
GENOMIC STRUCTURE
22 pairs of chromosomes are independent of sex, they are called
autosomes
GENOMIC STRUCTURE
The total chromosome count in a human is __ autosomes and two sex chromosomes, XX for females and XY
44
T/F: HUMAN GENETIC VARIATION
The differences (genetic polymorphisms) are what makes each individual unique (except identical twins)
T
Basic concepts of human genetic variation
–Locus
–Allele
–Polymorphism
–Mutation
refers to the position or location of a gene in the genome
Genetic Locus
are defined by chromosomal location, using chromosome bands (G-band or R-band) or molecular markers (microsatellites) as a point of reference.
Genetic Locus
is the “version” of a gene that is present at any given locus.
Allele
T/F: Allelic differences are related to alterations in the nucleotide sequence of a gene.
T
Position or location of a gene or genetic marker on a chromosome
Locus
Alternative versions of a gene at a given locus
Allele
