model organisms
species that are easy to raise in the lab and use in experiments
differentiation
the process by which cells become specialized in structure and function
morphogenesis
the physical processes that give an organism its shape
the development of the form of an organism and its structures
cytoplasmic determinants
maternal substances in the egg that influence the course of early development
induction
most influential are the signals communicated to an embryonic cell from other embryonic cells in the vicinity, including contact with cell-surface molecules on neighboring cells and binding of growth factors secreted by neighboring cells
such signals cause changes in the target cells, a process called induction
determination
refers to the unseen events that lead to the observable differentiation of a cell
tissue specific proteins
proteins found only in a specific cell type and give the cell its characteristic structure and function`
apoptosis
“programmed cell death”
occurs in cells of the mature organism that are infected, damaged, or have reached the end of their functional life span
pattern formation
development of a spatial organization in which the tissues and organs of an organism are all in their characteristic places
positional information
molecular cues that control pattern information
provided by cytoplasmic determinants and inductive signals
nurse cells & follicle cells
supply the egg with nutrients, mRNAs, and other substances needed for development, and make the egg shell
homeotic genes
genes that control pattern formation in the late embryo, larva, and adult
embryonic lethals
mutations affecting a process as fundamental as segmentation would surely be embryonic lethals, mutations with phenotypes causing death at the embryonic or larval stage
maternal effect gene
gene that, when mutant in the mother, results in a mutant phenotype in the offspring, regardlesss of the offspring’s own genotype
egg-polarity gene
another word for maternal effect gene:
gene that, when mutant in the mother, results in a mutant phenotype in the offspring, regardlesss of the offspring’s own genotype
bicoid
an embryo whose mother has 2 muant alleles of the bicoid gene lacks the front half of its body and has posterior structures at both ends
bicoid gene is essential for setting up the anterior end of the embryo
morphogens
substances that establish an embryo’s axes and other features of its form
totipotent
a cell with the potential to “dedifferentiate” and then give rise to all the specialized cell types of the organism
stem cell
relatively unspecialized cell that can both reproduce itself indefinitley and, under appropriate conditions, differentiate into specialiszed cells of one or more types
pluripotent
capable of differentiating into many cell types
CC
the first cloned cat
the two cats are not identical due to random X chromosome inactivation
oncogenes
cancer causing genes
proto-oncogenes
code for proteins that stimulate normal cell growth and division
Genetic changes that convert proto-oncogenes into oncogenes
movement of DNA within the genome
amplification of a proto-oncogene
point mutations in a control element or in the proto-oncogene itself
tumor-suppressor genes (+functions+
encode proteins that help prevent uncontrolled cell growth
- repair damaged DNA
- control the adhesion of cells
- inhibit the cell cycle
ras gene
codes for the ras protein, a G protein that relays a signal from a growth factor receptor on the plasma membrane to a cascade of protein kinases. the cellular response at the end of the pathway is the synthesis of a protein that stimulates the cell cycle
this process would not operate unless triggered by the appropriate growth factor
p53 gene
the protein it encodes for is a specific transcription factor that promotes the synthesis of cell cycle-inhibiting proteins
a mutation that knocks out the p53 gene, can lead to cancer
BRCA1 and BRCA2
mutations in the BRCA1 gene were associated with increasing suscpetability to breast cancer
mutations in that gene or the related BRCA2 gene are found in at least half of inherited breast cancers, and tests using DNA sequencing can detect these mutations
virus
infections particle consisting of little more than genes packaged in a protein coat
classification of viruses
their genomes may consist of
- double stranded DNA
- single stranded DNA
- double stranded RNA
- single stranded RNA
capsid
protein shell enclosing the viral genome
depending on the type of virus, the capsid may be rod-shaped, polyhedral, or more complex in shape
capsids are built from a large number of protein subunits called capsomeres
Tobacco mosaic virus
has a helical capsid wiht the overall shape of a rigid rod
adenoviruses
have an icosahedral capsid with a glycoprotein spike at each vertex
influenza virus
have eight different RNA molecules, each wrapped in a helical capsid, and an outer envelope studded with glycoprotein spikes
Bacteriophage
has a complex capsid consistign of an icosahedral head and a tail apparatus
viral envelopes
derived from the membranes of the host cell
contain host cell phospholipids and membrane proteins
host range
each particular virus can infect only a limited number of host species
lytic cycle
a phage replicative cycle that culminates in death of the host cell
virulent phage
a phage that replicates only by the lytic cycle
restriction enzymes
when phage DNA does enter a bacterium, the DNA often is identified as foreign and cut up by cellular enzymes called restriction enzymes, which are so named because their activity restricts the ability of the phage to infect the bacterium
lysogenic cycle
allows replication of the phage genome without destroying the host
temperate phages
phages capable of using both modes of replicating within a bacterium
prophage
when integrated into the bacterial chromosome, the viral DNA is known as a prophage
retroviruses
RNA animal viruses with the most complicated replicative cycles
use RT
reverse transcriptace
(RT) transcribes an RNA template into DNA, providing an RNA-> DNA information flow, the opposite of hte usual direction
HIV
retrovirus that causes AIDS
provirus
integrated viral DNA from HIV, never leaves the host’s genome, remaining a permanent resident of the cell
vaccine
harmless variant or derivative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen
ermerging viruses
viruses that suddenly become apparant
epidemic
general outbreak
pandemic
global epidemic
three processes contribute to the emergence of viral diseases
mutation of existing viruses
dissemination of a viral disease from a small, isolated human population
spread of existing viruses from other animals
horizontal transmission
a plant is infected with a virus from an external source
vertical transmission
the plant inherits a viral infection from a parent
genomics
studying whole sets of genes and their interactions
bioinformatics
the application of computational methods to the storage and analysis of biological data
Human genome progect
sequencing of the human genome beginning in 1990
whole-genome shotgun approach
J. Craig Venter developed this
starts with the cloning and sequencing of DNA fragments from randomly cut DNA, powerful computer programs then assemble the resulting very large number of overlapping short sequences into a single continuous sequence
metagenomics
DNA from a group of species is collected from an environmental ssample and sequenced
National library of Medicine and the National Institutes of health
United states organizations
Created the National center for biotechnology information (NCBI) which maintains a website with extensive bioinformatics resources
European molecular biology laboratory
europe
DNA data bank
Japan
BGI
Beijing Genome institute in Shenzhen, China
proteomics
study of the full protein sets encoded by genomes
systems biology
aims to model the dynamic behavior of whole biological systems
microarray chip
tiny spots of DNA arranged in a grid on this silicon wafer represent almost all of the genes in the human genome. using this chip, researchers can analyze the expression patterns for all these genes at the same time
E. Coli genome sizes and estimated numbers
Haploid Genome Size=4.6
Number of Genes=4,400
Genes per Mb=950
Yeast genome sizes and estimated numbers
Saccharomyces cerevisiae
Haploid Genome size=12
Number of genes=6,300
Genes per Mb=525
Drosophila melanogaster genome sizes and estimated numbers
Haploid Genome size=165
Number of genes=17,000
Genes per Mb= 84
mus musculus (House mouse) genome sizes and estimated numbers
Haploid Genome size=2,600
Number of Genes= 22,000
Genes per Mb= 11
Humans
Haploid genome size=3,000
number of genes=<21,000
genes per Mb=7
percent that codes for exons
1.5%
pseudogenes,
former genes that have accumulated mutations over a long time and no longer produce functional proteins
repetitive DNA
consists of sequences that are present in multiple copies in the genome
75% of repetitive DNA (44% of genome) is made of transposable elements
transposable elements
stretches of DNA that can move from one location to another within the genome
Barbara McClintock
experiments with Indian corn discovered transposable elements
transposons
can move within a genome by means of a DNA intermediate
-cut and paste
-copy and paste
both mechanisms require the enzyme transposase, which is generally econoded by the transposon
retrotransposons
move by means tof an RNA intermediate htat is a transcript of retrotransposon DNA
always leave a copy at the original site
use reverse transcriptase
simple sequence DNA
contains many copies of tandemly repeated short sequences
short tandem repeat (STR)
when the repeated unit contains 2-5 nucleotides,
multigene families
collections of 2 or more identical or very similar genes
domains
proteins often have a modular architecture consisting of discrete structural and functional regions called domains
exon shuffling
could have moved exons from ancestral forms of the genes for epidermal growth factor, fibronectin, and plasminogen into the evolving gene for tissue plasminogen activator, TPA. duplication of an exon could account for the increased neeed for the protein it codes for
highly conserved
genes have remained similar
FOXP2
vocalization
- both genes=normal vocalization
- one gene=some vocalization
- no genese=no vocalization
single nucleotide polymorphisms
single base-pair sites where variation is found in at least 1% of the population
evo-devo
evolutionary developmental biology
compare developmental processes of different multicellular organisms
homeobox
180-nucleotide sequence, which specifies a 60-amino acid homeodomain in the encoded proteins
hox genes
homeotic genes in animals