BIO 358 Lecture Notes - Lecture 3: Combinatoriality, Dna Replication, Molecular Machine
14 Jun 2018
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Topic 3:
Key Terms:
1. Combinatoriality: combinatorial: For our purposes this term refers to the use of combinations of limited
numbers of symbols or elements (or their equivalent) to encode information or to build complexity. For
example, the letters of the alphabet are used to combinatorially encode written language. Also, for example,
our phone number system is combinatorial. See Chapter 2 for a discussion of the use of combinatoriality to
build complex biological structures and to encode information.
2. Monomer:
3. Polymer:
4. DNA: Abbreviation for the chemical name of the polymer that encodes genetic design information
(deoxyribonucleic acid). See Chapter 2 for a discussion of the issues summarized here. This polymer is made of
a linear (unbranched) string of monomers. These individual monomer units are the DNA bases abbreviated A,
T, G and C for the first letters of their chemical names. The following properties of DNA are relevant to us
here. First, because the monomer units making up DNA are slightly different from one another, the sequence
of these monomers can be used to encode information, generally analogously to the use of letters to encode
words and sentences in written language. The information so encoded is genetic design information. Second,
this information can be used to control the sequence of amino acid monomers in the proteins encoded by
DNA sequences. The twenty amino acids normally used are each different chemically from one another so that
the protein polymer is richly complex in structure. Typically the protein polymer folds up into a complex three
dimensional object which can function as a molecular machine if so designed by natural selection. These
protein molecular machines and structural components are the major class of tool molecules in the
contemporary biological vehicles or organisms (Chapter 2). DNA sequence is copied into a similar, but
disposable molecule called RNA by a process called transcription. This RNA transcript, in turn, is used to direct
the synthesis of a protein (according to the genetic code) through a process referred to as translation. Third,
the DNA bases pair with one another in very specific ways so that one chain of DNA can be used as a template
to make a new DNA chain of controlled sequence. This constitutes replication of genetic design information.
Thus, DNA encodes genetic design information that builds vehicles (organisms consisting of the DNA itself plus
all the tools for its replication). Animals like us are very complex vehicles built by genetic design information
shaped by Darwinian or natural selection.
5. RNA:
6. Protein:
7. Transcription, translation and DNA replication:
8. Nucleotide (base):
9. Amino acid:
10. Genomes: The technical term for all the genetic design information directing the building of a specific
organism (vehicle). Contemporary genomes include many pieces of design information which interact
combinatorially to produce the complexity of the organisms we see. Also see chromosome, DNA, haploid and
diploid.
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11. Organelle: Refers to relatively large structures within cells which carry out specific functions and typically
consist of many copies of large machines generally containing dozens of proteins and, often, other molecules.
Organelles include the nucleus in which genetic design information is stored in contemporary animals. These
also include a variety of other structures like the mitochondria where key steps in energy metabolism occur or
the Golgi apparatus where protein gene products are prepared for secretion to the outside world.
KEY CONCEPT QUESTION: Our ability to understand the origin and logic of the anatomy and behavior of all
organisms (ultimately including humans) depends ABSOLUTELY on our ability to comprehend how evolution
by natural selection works. Which of the following statements most accurately and completely describes the
essential properties of evolution by natural selection?
a. Randomly arising changes in design information compete for limited opportunities to replicate in a crowded
environment, leading to the evolution of anatomy and behavior.
b. Randomly arising changes in design information usually improve the design of the organism, leading to the
evolution of anatomy and behavior.
c. Changes in design information deliberately produced by an evolved mechanism, improve the design of the
organism, leading to evolution of anatomy and behavior.
d. Changes in design information deliberately produced by an evolved mechanism compete for limited
opportunities to replicate in a crowded environment, leading to the evolution of anatomy and behavior.
Notes:
1) Evolving genes and the animals they build
a) Do not focus on vehicle, focus on the encoded information
i) Orgaiss are ople ehiles uilt desig iforatio for the purpose of repliatig that
information
(1) Organisms are just self-replicating shirts
(2) We ill talk aout purpose i the o-human sense
(a) For non-human social behavior is built mostly from design info
(b) The central role of information in the biology of organisms
(c) A physical law governing accuracy of information replication
(i) Understanding evolution by natural selection
(d) The competitive nature of design information replication
(e) How natural selection emerges as a blind, mechanical process from these properties of the
chemical world
(i) Just as mechanical as the bouncing of a rubber ball
(f) Hierarchically nested combinatoriality and the structure of animal bodies
ii) Biological organisms heial ehiles are aout iforatio
(1) DNA double helix
(a) Just know that information is coded in a linear fashion, there is a 4 letter code (ATGC),
complementarity rules that allow linear segments in the code to copy themselves
(b) You resemble your parents bc you have their information coded
iii) The “eod La ad iologial iforatio
(1) Precise information is continually degraded
(a) You must keep giving it energy to keep it the way it should be (good as new)
(2) If you want to replicate design information, and you want to do it with infinite precision (never
make a dna replicating mistake), you have to invest infinites amount of energy.
(a) Orgaiss do’t hae ifiites aout of eerg, so the ake tradeoffs
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Document Summary
Key terms: combinatoriality: combinatorial: for our purposes this term refers to the use of combinations of limited numbers of symbols or elements (or their equivalent) to encode information or to build complexity. For example, the letters of the alphabet are used to combinatorially encode written language. Also, for example, our phone number system is combinatorial. See chapter 2 for a discussion of the use of combinatoriality to build complex biological structures and to encode information: monomer, polymer, dna: abbreviation for the chemical name of the polymer that encodes genetic design information (deoxyribonucleic acid). See chapter 2 for a discussion of the issues summarized here. This polymer is made of a linear (unbranched) string of monomers. These individual monomer units are the dna bases abbreviated a, T, g and c for the first letters of their chemical names. The following properties of dna are relevant to us here. The information so encoded is genetic design information.
