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AP Bio- Regulation 1: Genetics- Systems Perspectives

1 of 7 of Regulation Domain (two discussions) Credit:Biology (Campbell) 9th edition, copyright Pearson 2011, & The Internet. Provided under the terms of a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. By David Knuffke.
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David Knuffke

on 9 December 2014

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Transcript of AP Bio- Regulation 1: Genetics- Systems Perspectives

Genetics:
A Systems Perspective
Developmental Genetics
Genomics
Differentiation
Pattern Formation
Developmental Regulators
Genome Sequencing
The Human Genome
Genome Evolution
Process
Analysis
To sequence a genome:
Shred it in to bits
Sequence the shreds
Use a computer to line it all back up
The Human Genome Project Method
Whole-Genome "Shotgun" sequencing
Vs.
Bioinformatics
:
Computational analysis
of genetic data
SUPER IMPORTANT!
2 Views of Genome Comparisons
An interaction map of 4,500 proteins in
S. cervisiae
(a yeast)
All protein & RNA coding sequences
~3 times more introns than exons!
Promoters, enhancers, etc.
Gene Fragments & "
Pseudogenes
"
STR's, larger repeats (up to 500 bases)
Big segments (thousands of bases), present in a few copies.
Most of the Y chromosome
A small retrotransposon found in all primates.
Transposable Elements!
Non-coding DNA segments that catalyze their own replication and movement throughout the genome

Discovered by Barbara McClintock in corn in 1940's. Nobel Prize in 1983.
Transposons:
Retrotransposons:
DNA sequences that code for their own replication/insertion
Transcribed into RNA and are reverse transcribed back in to DNA prior to insertion.
Code for their own Reverse Transcriptase.
Barbara McClintock demonstrated that corn kernel color inheritance could only be explained through mobile genetic elements (aka "jumping genes")
Now that all of this genome data exists, it can be analyzed for patterns.

Evolution should leave signatures in the data. What do those signature look like?
Gene Families
Refers to collections of genes with identical or similar structures.

Result from
duplication events
.

Following duplication, sequences may diverge in structure and function.
Identical sequence families
sequences of genes that occur multiple times in a genome.
usually cluster together in the genome.
example: rRNA genes (1000's of copies)
Non-identical sequence families
related, non-identical gene sequences.
can be found in different locations of the genome
example: alpha & beta globin genes
Duplication &
Divergence
Following a duplication of genetic information, gene sequences can mutate to acquire novel functions (or to become non-functional).

These processes occur at the chromosomal, gene, and intra-gene levels of genome organization.
Chromosomal
Alterations
Rearrangement of chromosome structures leaves signatures
Comparing Genomes
Looking at similarities and differences in genomes provides evidence for how evolution has changed the genetic structures of different species.
How do cells with the same genetic information acquire different structures and functions?
Cytoplasmic Determinants
Substances present in the cytoplasm of the egg cell that are unevenly distributed

Direct different gene expression in subsequent generations of cells.

Important in early development
Induction
Signals from surrounding cells that determine the course of a cell's genetic development.

Important in later development.
Determination
The regulatory events in a cell's genome that lead to differentiation of structure and function.

Once a cell commits to a particular fate, it can not uncommit.

Determination precedes differentiation.
How is a body plan established in a developing organism?
Positional Information
The molecular signals that establish the body axes in a developing organism.

Much of the work on genetic development was done in
Drosophila
.
Lots of work, done over a long period of time.

We'll look at one specific example.
Homeotic
Genes
Bicoid: An Example
Bicoid
is a protein that is present in a differential gradient in the unfertilized egg.

Cells that develop in a high concentration of bicoid become the anterior (head) of the organism.

Bicoid controls head development directly, so it is referred to as a "
morphogen
".
First discovered in
Drosophila
by Edward B. Lewis. Nobel Prize in 1995

Have since been discovered in all animal lineages.

Highly conserved sequences (what does that mean), including a characteristic "box" of bases called a "
homeobox
"
Big Questions
Make Sure You Can:
How does genetics contribute to the development of an organism?


How does evolution influence the structure of an organism's genetic code?
Clearly, something pretty important has to happen to get from (a) to (b)
Simplified diagram of determination leading to differentiation in a muscle cell
Morphological differences between normal (top) and
bicoid
mutant (bottom) fruit fly larvae
Distribution of
bicoid
in normal fruit fly egg and early-stage embryo
Antennapedia
mutants have legs in the wrong places
Eyeless
mutants have vestigial eyes in odd places
It quickly becomes clear why these experiments are done in fruit flies
While vertebrates have more
Homeotic
genes than invertebrates, the sequences are very highly conserved.
Differences in
homeobox
expression patterns lead directly to differences in segmentation
Florescence image showing 7 different
homeobox
expression patterns in a fruit fly embryo.
Tools like microarrays make system-level analysis much easier.
Technology has made genome sequencing less and less costly
Translocations during crossing over
Evidence of chromosomal fusions are found in the human genome when compared to other mammalian lineages
Correlating genetic changes to fossil evidence allows for approximate dating of genetic divergence among organisms
Analysis of amino acid sequences can inform evolutionary hypotheses
Sequence analysis suggests that the current
TPA
gene resulted from transposition of exons from three different genes.
The
FOXP2
gene seems to be involved in language in humans. It is related to the development of various structures in the brain.
Development:
Explain the role of cytoplasmic determinants and induction in contributing to development.
Describe the relationship between determination and differentiation in a cell.
Explain how positional information is conveyed to the cells in a developing organism.
Explain the role of homeotic genes in contributing to the development of an animal.
Genomics:
Explain how genomes are sequenced.
Explain the role of bioinformatics in genomic analysis.
Compare trends in the evolution of genomes.
Describe the structure and function of transposable elements, simple sequence DNA, regulatory elements and exons in the human genome, and their relative precentages.
Explain the genetic events that have led to the evolution of multi-gene families.
Provide examples of evidence from genomic analysis that supports the evolution of humans from a common ancestor with apes, and other mammals.
Explain how a duplication of genetic information can lead to the evolution of new genes with novel functions.
Regulatin' Genes
Shotgun Sequencing
Original HGP Procedure
What the Human Genome Looks Like
Full transcript