BIO Module 7 (Exam 2)

Genomes, Genomics, and genetic variation

Genome

all the genetic material in an organism

Smallest genome

viral genome (viruses)

DNA Based Genome

prolaryotic and eukaryotic genomes are DNA-based

genome size is measure by..

number of nucleotides or base pairs

Viral shapes

• Helical

• polyhedral

• spherical

• complex

Helical

Cylinder -like

• tobacco, mosaic virus

Polyhedral

Hexagonal

• adenovirus

Spherical

Circle shape

• influenza

• covid

Complex

• bacteriophage

Number of base pairs (Bacterial genomes)

500,000 to 10 million base pairs

• depends on “life style”

Genomics

an interdisciplinary field of biology focused on the structure, function, evolution, mapping and editing of genomes

3 fundamental components of genomic research

1. genome sequencing

2. genome assembly

3. genome annotation

Molecular Biology

identify genes and the proteins they encode

identify non-coding regions of the genome and their regulatory functions

Metagenomics

identify all organisms in an environmental sample or microbiome

Virology

identify and study viruses for vaccine development

Medicine

identify genetic risk factors and best treatments

Forensic

identify paternity and individuals in criminal investigations

Evolutionary Biology

identify the evolutionary history of species

Coserving wildlife

identify population genetic diversity and health

DNA sequencing methods

• Sanger Method

• Next generation sequencing (NGS)

Sanger Method

• 1977

Chain termination Method

• commercialized in 1987: still used today because of itsb low error rate

Next generation sequencing

• Available since 2004 and largely replaced sanger sequencing

• NGS technology makes high-throughput whole-genome sequencing (WGS) possible

Polymerase Chain Reaction (PCR)

A fundamental and broadly applied technique for amplifying/replicating DNA

• used to exponentially increase the number of copies of DNA so that genes and genomes may be studied in greater detail

PCR steps

• denturation

• annealing

• extension

Denaturation

temperature is increased to separate DNA strands

Annealing

temperature is decreased to allow primers to base pair to complementary DNA template

Extension

polymerase extends primer to form nascent DNA strand

Shotgun sequences

still no technology for the sequencing and assembly of an entire genome as one continuous sequence

• break apart DNA and put it back together

Structural annotation

identification of genomic elements (ex: protien-coding genes, non-coding DNA) and their locations within the genome

Functional annotation

attaching biological information to genomic elements

mutation

any change in the genetic material of an organism. Fundamental source of genetic variation that produces new phenotypes (physical traits)

Somatic Cell

mutation rates per cell cycle are higher but they are NOT heritable across generations. Mutations are inherited only within the cell lineage that they arise

Germ cells

Mutations accumulate and are then passed on to sperm/egg during Meiosis. These ARE heritable across generations

pseudogenes

a section of a chromosome that is an imperfect copy of a functional gene

colon cancer

the accumulation of three successive mutations in a lineage of colon cells

Lederberg experiment 1952

• random mutations in bacteria that produced antibiotic resistance

• also discovered bacterial conjugation

types of mutations

1. small scale

2. large scale

Small scale mutations

• point mutation (nucleotide substitution)

  • synonymous (silent) mutations

  • nonsynonymous (missense) mutations

  • nonsense mutations

• nucleotide insertions/deletion (indel)

Large scale mutations (chromosomal mutations)

• single chromosome mutation

• two chromosome mutation

Synonymous Mutation (silent)

Does NOT change the amino acid

nonsynonymous mutation (missense)

Does change the amino acid

• sickle cell anemia

Nonsense Mutation

Creates a STOP codon

Nucleotide Insertion

• frameshift mutation

That is not an exact multiple of 3 nucleotides changes the reading frame of translation

Nucleotide deletion

• cause of cystic fibrosis

Single chromosome mutations

• one chromosome

Deletion, duplication, Inversion

Two chromosome Mutation

Insertion and translocation

Discrete genetic variations

• polymorphism

• Single-nucleotide polymorphism (SNP)

• variable number of tandem repeats (VNTR)

• Short Tandem Repeat (STR)

Polymorphism

discontinuous genetic variation resulting in the occurrence of several different forms or types among members of a single species

Single-nucleotide polymorphism (SNP)

A substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of the population

variable number of tandem repeats (VNTR)

repetitive elements may comprise 2/3 of human genome but are variable from one person to another

Short tandem repeat (STR)

• STR polymorphisms are used in DNA fingerprinting

• STR sequences range from 2 to 16 bp in length

• individuals have different alleles for an STR site based on the # of repeats in their sequence

Gel electrophoresis

Ubiquitous method for separating and analyzing macromolecules based on their size and charge

• DNA fragments move through gel toward positive elctrode

• smaller fragments move faster/farther

• Used to identify STR alleles in each individual based on size/length of those alleles

Copy number variation (CNV)

• the result of deletions and insertions

• the size of the duplicated or deleted region can include one or more complete genes

• 5-10% of human genome is due to CNV

• much larger sequences than SNPs