This document provides an overview of key concepts from Chapter 21 of Campbell Biology about genomes and their evolution. It discusses the stages of genome sequencing, including genetic mapping, physical mapping, and DNA sequencing. It also describes how new sequencing techniques like whole-genome shotgun sequencing have accelerated the process. Bioinformatics tools are now used to analyze whole genomes and understand gene functions on a systems level. Comparisons of complete genome sequences from different organisms reveal variation in genome size, number of genes, and amount of noncoding DNA between domains of life.
Cloning is the process of producing genetically identical individuals of an organism either naturally or artificially.
It is the process of taking genetic information from one living thing and creating identical copies of it. The copied material is called a clone.
Nature has been doing it for millions of years. For example, identical twins have almost identical DNA, and asexual reproduction in some plants and organisms can produce genetically identical offspring.
Cloning in biotechnology refers to the process of creating clones of organisms or copies of cells or DNA fragments (molecular cloning).
The chain-termination method developed by Frederick Sanger and coworkers in 1977. This method used fewer toxic chemicals and lower amounts of radioactivity than the Maxam and Gilbert method. Because of its comparative ease, the Sanger method was soon automated and was the method used in the first generation of DNA sequencers.
lecture for doctorate students while I was working as researcher assisstance about phylogenetic science, definition,
Understand the most basic concepts of phylogeny
Understand the difference between orthology, paralogy and xenology.
Be able to compute simple phylogenetic trees
Understand what bootstrapping means in phylogeny
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
Cloning is the process of producing genetically identical individuals of an organism either naturally or artificially.
It is the process of taking genetic information from one living thing and creating identical copies of it. The copied material is called a clone.
Nature has been doing it for millions of years. For example, identical twins have almost identical DNA, and asexual reproduction in some plants and organisms can produce genetically identical offspring.
Cloning in biotechnology refers to the process of creating clones of organisms or copies of cells or DNA fragments (molecular cloning).
The chain-termination method developed by Frederick Sanger and coworkers in 1977. This method used fewer toxic chemicals and lower amounts of radioactivity than the Maxam and Gilbert method. Because of its comparative ease, the Sanger method was soon automated and was the method used in the first generation of DNA sequencers.
lecture for doctorate students while I was working as researcher assisstance about phylogenetic science, definition,
Understand the most basic concepts of phylogeny
Understand the difference between orthology, paralogy and xenology.
Be able to compute simple phylogenetic trees
Understand what bootstrapping means in phylogeny
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
Introduction to Synthetic Genome
SYNTHETIC GENOMICS Study of Invitro chemical synthesis of genetic material i.e., DNA in the form of oligonucleotides, genes, or genomes with Computational techniques for its design. SYNTHETIC GENOME Artificially synthesised genome (invitro)
Microbiology has experienced a transformation during the last 25 years that has altered microbiologists' view of microorganisms and how to study them. The realization that most microorganisms cannot be grown readily in pure culture forced microbiologists to question their belief that the microbial world had been conquered. We were forced to replace this belief with an acknowledgment of the extent of our ignorance about the range of metabolic and organismal diversity.
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
14. Cut the DNA into
overlapping frag-
ments short enough
for sequencing.
1
Clone the fragments
in plasmid or phage
vectors.
2
Figure 21.3-1
15. Cut the DNA into
overlapping frag-
ments short enough
for sequencing.
1
Clone the fragments
in plasmid or phage
vectors.
2
Sequence each
fragment.
3
Figure 21.3-2
16. Cut the DNA into
overlapping frag-
ments short enough
for sequencing.
1
Clone the fragments
in plasmid or phage
vectors.
2
Sequence each
fragment.
3
Order the
sequences into
one overall
sequence
with computer
software.
4
Figure 21.3-3
27. Translation and
ribosomal functions
Nuclear-
cytoplasmic
transport
RNA processing
Transcription
and chromatin-
related functions
Mitochondrial
functions
Nuclear migration
and protein
degradation
Mitosis
DNA replication
and repair
Cell polarity and
morphogenesis
Protein folding,
glycosylation, and
cell wall biosynthesis
Secretion
and vesicle
transport
Metabolism
and amino acid
biosynthesis
Peroxisomal
functions
Glutamate
biosynthesis
Serine-
related
biosynthesis
Amino acid
permease pathway
Vesicle
fusion
Figure 21.5
28. Figure 21.5a
Translation and
ribosomal functions
Nuclear-
cytoplasmic
transport
RNA processing
Transcription
and chromatin-
related functions
Mitochondrial
functions
Nuclear migration
and protein
degradation
Mitosis
DNA replication
and repair
Cell polarity and
morphogenesis
Protein folding,
glycosylation, and
cell wall biosynthesis
Secretion
and vesicle
transport
Metabolism
and amino acid
biosynthesis
Peroxisomal
functions
41. Figure 21.7
Exons (1.5%) Introns (5%)
Regulatory
sequences
(∼20%)
Unique
noncoding
DNA (15%)
Repetitive
DNA
unrelated to
transposable
elements
(14%)
Large-segment
duplications (5−6%)
Simple sequence
DNA (3%)
Alu elements
(10%)
L1
sequences
(17%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
74. Exon
duplication
Exon
shuffling
Exon
shuffling
F EGF K K
K
F F F F
EGF EGF EGF EGF
Epidermal growth
factor gene with multiple
EGF exons
Fibronectin gene with multiple
“finger” exons
Plasminogen gene with a
“kringle” exon
Portions of ancestral genes TPA gene as it exists today
Figure 21.15
79. Most recent
common
ancestor
of all living
things
Bacteria
Eukarya
Archaea
Chimpanzee
Human
Mouse
Millions of years ago
Billions of years ago
4 3 2
010203040506070
01
Figure 21.16
84. EXPERIMENT
Wild type: two normal
copies of FOXP2
RESULTS
Heterozygote: one
copy of FOXP2
disrupted
Homozygote: both
copies of FOXP2
disrupted
Experiment 1: Researchers cut thin sections of brain and stained
them with reagents that allow visualization of brain anatomy in a
UV fluorescence microscope.
Experiment 1 Experiment 2
Experiment 2: Researchers separated
each newborn pup from its mother
and recorded the number of
ultrasonic whistles produced by the
pup.
Wild type Heterozygote Homozygote
Numberofwhistles
400
300
200
100
0
Wild
type
Hetero-
zygote
Homo-
zygote
(No
whistles)
Figure 21.17
85. EXPERIMENT
Wild type: two normal
copies of FOXP2
RESULTS
Heterozygote: one
copy of FOXP2
disrupted
Homozygote: both
copies of FOXP2
disrupted
Experiment 1: Researchers cut thin sections of brain and stained
them with reagents that allow visualization of brain anatomy in a
UV fluorescence microscope.
Experiment 1
Wild type Heterozygote Homozygote
Figure 21.17a
86. Wild type: two normal
copies of FOXP2
Heterozygote: one
copy of FOXP2
disrupted
Homozygote: both
copies of FOXP2
disrupted
Experiment 2: Researchers separated each newborn pup from its mother
and recorded the number of ultrasonic whistles produced by the pup.
Experiment 2
Numberofwhistles
400
300
200
100
0
Wild
type
Hetero-
zygote
Homo-
zygote
(No
whistles)
EXPERIMENT
RESULTS
Figure 21.17b
101. Archaea
Most are 1−6 Mb
Eukarya
Genome
size
Number of
genes
Gene
density
Introns
Other
noncoding
DNA Very little
None in
protein-coding
genes
Present in
some genes
Higher than in eukaryotes
1,500−7,500 5,000−40,000
Most are 10−4,000 Mb, but a
few are much larger
Lower than in prokaryotes
(Within eukaryotes, lower
density is correlated with larger
genomes.)
Unicellular eukaryotes:
present, but prevalent only in
some species
Multicellular eukaryotes:
present in most genes
Can be large amounts;
generally more repetitive
noncoding DNA in
multicellular eukaryotes
Bacteria
Figure 21.UN01
102. Protein-coding,
rRNA, and
tRNA genes (1.5%)
Human genome
Introns and
regulatory
sequences (∼26%)
Repetitive DNA
(green and teal)
Figure 21.UN02
103. Figure 21.UN03
α-Globin gene family
Chromosome 16
β-Globin gene family
Chromosome 11
βζ ψζ ψα 2
ψα 1
α2 α1 ψθ ε G Aγ γ ψβ δ