Genetics is a PLAN for life

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Learning goals Lecture 6, Genetic information
Text Reading Download extra file on web site on
What you need to know about DNA. The Figures
that you should look at can be found in this
lecture file.
You need to be able to explain the following to
yourself and to me (on exams)
Genetics is a PLAN for life What is genetics
why it is important, genetic plans genetic
reality vs analogy what you need to know about
molecular genetics in this class Essential
molecular genetics An analogy DNA, base,
nucleotide, protein, amino acid, enzyme, mRNA,
transcription, translation, gene experssion
Genomes are organized differently in different
species what is a genomes, eukaryotic
prokaryotic, chromosome nuclear DNA
extranuclear DNA, genome project DNA sequencing,
bioinformatics Kilobase (kb), megabase, species
differences in genomes  
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• Comments
• Please finish studying Lecture 5 on your own - we
  need to go ahead and stay on schedule.
• I have not listed all the book Figures in the
  reading - they can be found in the lecture file.

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Genetics is a PLAN for life what is genetics why
it is important genetic plans reality vs
analogy molecular genetics in this class
What is genetics? Book (glossary) definition -
the scientific study of heredity and hereditary
variations But what does hereditary mean?
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Genetics is a PLAN for life what is genetics why
it is important genetic plans reality vs
analogy molecular genetics in this class
What is genetics? Book (glossary) definition -
the scientific study of heredity and hereditary
variations What does hereditary mean? -
something is hereditary if it is passed from one
generation (organisms alive at one point in
time) to the next generation.
You are an individual organism
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Genetics is a PLAN for life what is genetics why
it is important genetic plans reality vs
analogy molecular genetics in this class
What is genetics? Book (glossary) definition -
the scientific study of heredity and hereditary
variations What does hereditary mean? -
something is hereditary if it is passed from one
generation (organisms alive at one point in time)
to the next generation. An idea from me
Genetics is the study of how life goes on, even
though individual organisms die.
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Genetics is a PLAN for life what is genetics why
it is important genetic plans reality vs
analogy molecular genetics in this class
Why is understanding genetics important? It is
major intellectual problem (question) It has huge
practical implications (cancer, hereditary
diseases, crop domestication, etc.)
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Genetics is a PLAN for life what is genetics why
it is important genetic plans reality vs
analogy molecular genetics in this class
If Genetics is the study of how life goes on,
even though individual organisms die, then what
exactly is passed on? What is passed from one
generation to the next are the plans for life.
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Genetics is a PLAN for life what is genetics why
it is important genetic plans reality vs
analogy molecular genetics in this class

• What would we like to see in a genetic plan?
• Physical durability
• A foolproof (as much as possible) way to store
  and read the plans

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Genetics is a PLAN for life what is genetics why
it is important genetic plans reality vs
analogy molecular genetics in this class

• What would we like to see in a genetic plan?
• Physical durability
• A foolproof (as much as possible) way to store
  and read the plans

• The solution that life has come up with is to put
  the plans for life in a
• Linear (string-like) form
• With information stored digitally - has high copy
  fidelity

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Genetics is a PLAN for life what is genetics why
it is important genetic plans reality vs
analogy molecular genetics in this class

• We can approach genetic plans in two different
  ways
• Reality - DNA
• Analogy - CDs, written text

Both approaches have their value, although
obviously we need to teach you a great deal about
the reality of genetics.
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Genetics is a PLAN for life what is genetics why
it is important genetic plans reality vs
analogy molecular genetics in this class
One of the realities of genetics is that it it is
based in molecular (chemical) biology.
Therefore, we will overlap some with MCB 150.
translation
genetic maps
DNA
meiosis
cancer
gene
population genetics
gene regulation
IB 150
MCB 150
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Genetics is a PLAN for life what is genetics why
it is important genetic plans reality vs
analogy molecular genetics in this class
Read What you need to know about DNA, online at
course web site, http//www.life.uiuc.edu/ib/150/
Our focus only what you need to know about DNA
to understand the part of genetics in IB 150.
translation
genetic maps
DNA
meiosis
cancer
gene
population genetics
gene regulation
IB 150
MCB 150
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Molecular genetics an analogy DNA protein,
enzyme transcription, translation expression

• How to store the plan for life
• Linear (string-like) form
• With information stored digitally

We need to start with DNA, the most important
molecule of genetics and life. But I will start
with an analogy.
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Molecular genetics an analogy DNA transcription,
translation expression
An analogy for DNA - storage of music in a
linear, digital form. The stored form doesnt
look like music, does it?
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Molecular genetics an analogy DNA protein,
enzyme transcription, translation expression
Analogy continued - there can be more than 3
stages in the process of playing digital music.
A computer hard drive doesnt look like a musical
instrument, does it?
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Molecular genetics an analogy DNA protein,
enzyme transcription, translation expression
The linear, digital view of genetic plans, and
the central role of DNA as a way to store
information on how to make life. Notice that the
information goes through three steps.
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The Structure of Nucleic AcidsNote what you Need
to Know -base, sugar, phosphate, nucleotide,
polymer
Molecular genetics an analogy DNA protein,
enzyme transcription, translation expression

• Nucleic acids
• Exist as polymers (molecule made of repeated
  units) called polynucleotides

(a) Polynucleotide, or nucleic acid
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Figure 5.29 The components of nucleic acids
Know that there are 4 bases, 2 pyrimidines (1
ring) cytosine, C, thymine, T, 2 purines
(2-ring), adenine, A, and guanine, G. You do not
have to know detailed structures!
Molecular genetics an analogy DNA protein,
enzyme transcription, translation expression
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Molecular genetics an analogy DNA protein,
enzyme transcription, translation expression
DNA is a double polymer, linked by hydrogen
bonds. Fig. 16.7. Focus on double-strand double
helix, and base-pairing, with hydrogen bonds.
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Molecular genetics an analogy DNA protein,
enzyme transcription, translation expression
Double-stranded DNA Base-pairing rules A
with T G with C purine with
pyrimidine 2-ring with 1-ring But no rules about
the sequence on a single strand - GTTACG is OK,
AAATGC is Ok, etc.
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Figure 5.30 The DNA double helix and its
replication
Molecular genetics an analogy DNA protein,
enzyme transcription, translation expression
Because of the base-pairing rules, DNA can
replicate itself and preserve the sequence of
bases.
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Molecular genetics an analogy DNA protein,
enzyme transcription, translation expression

• DNA alone is not life!
• To make life, DNA builds its plans using
  proteins.
• A protein is a polymer made of individual units
  called amino acids. There are 20 different amino
  acids. The sequence of amino acids is unique to
  each particular protein, and is essential for its
  function.
• Perhaps the three most important things to know
  about proteins is that they
• -Have a particular linear sequence of amino acid
  sequence that can be coded by DNA
• - Fold up into complex 3-D shapes
• Carry out many different functions

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Molecular genetics an analogy DNA protein,
enzyme transcription, translation expression
Fig. 5.19 - This is the protein lysozyme in two
different representations, both showing the
folding. The 3-D structure is needed for the
function of the protein.
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Molecular genetics an analogy DNA, base,
nucleotide protein, enzyme transcription,
translation expression

• The active site
• Is the region on the enzyme where the substrate
  binds

One very important function for proteins is to
act as enzymes - molecules that make a chemical
reaction go. The enzyme hexokinase takes a
glucose molecule (and an ATP molecule, not
shown), and makes glucose-6-phosphate, which then
can be broken down to provide energy.
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Molecular genetics an analogy DNA, base,
nucleotide protein, enzyme transcription,
translation expression

• The active site
• Is the region on the enzyme where the substrate
  binds

Enzyme and substrate make a temporary union, and
the chemical reaction goes forward.
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Figure 5.28 DNA? RNA ? protein a diagrammatic
overview of information flow in a cell
Molecular genetics an analogy DNA protein,
enzyme transcription, translation expression
Making a protein from the plans in the DNA is a
two step process.
Transcription A messenger RNA copy of the gene
is made (RNA has ribose instead of deoxyribose,
has uracil instead of thymine, and is single
stranded).
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Figure 5.28 DNA? RNA ? protein a diagrammatic
overview of information flow in a cell
Molecular genetics an analogy DNA protein,
enzyme transcription, translation expression
Making a protein from the plans in the DNA is a
two step process.
Translation The messenger RNA copy of the gene
is cranked through a ribosome, and the
information on protein sequence in the mRNA is
used to make a protein.
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Molecular genetics an analogy DNA, base,
nucleotide protein, enzyme transcription,
translation expression
Gene a segment of DNA that encodes (contains
the plans for) a single gene.
Quite a few simplifications here.
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Molecular genetics an analogy DNA, base,
nucleotide protein, enzyme transcription,
translation expression
The plans to make a protein are encoded in a
linear, digital code. An analogy - Morse code a
._ b _ c _._. d _.. abba ._ _ _ ._
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Molecular genetics an analogy DNA, base,
nucleotide protein, enzyme transcription,
translation expression

• The plans to make a protein are encoded in a
  linear, digital code.
• The reality - the universal genetic code
• Exceptions occur

Notice that the code is redundant - there are
more than one codons for some proteins.
OCH, AMB, and OPA are stop signals. Each set of
3 bases is called a codon.
Know the idea, and these terms - do not memorize
the code!
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Molecular genetics an analogy DNA, base,
nucleotide protein, enzyme transcription,
translation expression
All genes are not producing their proteins at
once! Life is very organized. When a gene is
producing its protein, it is said to be
EXPRESSED. Although gene expression is very
complicated, the most common way in which
expression occurs is for transcription to occur
or not. Proteins called transcription factors
regulate whether transcription occurs.
Transcription factors have a very precise 3-D
shape that allows them to fit to DNA. The
products of some genes regulate the expression of
several other genes, which in turn regulate
others, so there is a very complex set of gene
interactions throughout the life of an organism.

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Genomes terms genome projects species
differences extranuclear DNA
Genome the set of all genes plus other
(noncoding) DNA needed to encode the plans for a
given species of life
Chromosome a continuous length of DNA
Prokaryotes (bacteria) generally have one genome
per cell organized into one circular chromosome.
Eukaryotes (plants, animals, fungi) generally
have genomes organized into several non-circular
chromosomes, and often have two complete genomes
per cell (one from each parent). Most
chromosomes occur in a nucleus, but there are
also extracuclear chromosomes.
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Genome projects
Genomes terms genome projects species
differences extranuclear DNA

• Genome projects seek to discover all of the genes
  of an organism by sequencing all of an organisms
  DNA. Genome projects are multi-million dollar
  projects.
• Bioinformatics is the discipline that helps us
  decode the genome. Bioinformatics involves a
  great deal of computer analysis, as well as
  evolutionary biology, and often is housed in
  integrative biology departments.

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Genome comparisons
Genomes terms genome projects species
differences extranuclear DNA

• Amount of DNA ( base pairs)
• Number of genes
• Amount of coding DNA ()
• Number of chromosomes ( in somatic cells)

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Genomes terms genome projects species
differences extranuclear DNA
Genome Size
Notice the 5 orders of magnitude difference in
the number of base pairs in different genomes.
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Number of genes in sequenced genomes
Genomes terms genome projects species
differences extranuclear DNA

• HIV 10
• Mycoplasma 517
• E. coli 4,300
• Streptomyces 8,000
• Yeast 6,000
• Roundworm 18,000
• Fruit fly 14,000
• Mosquito 14,000
• Mouse 30,000
• Human 30,000
• Arabidopsis 25,000

But there is only about a 6-fold (one order of
magnitude) difference in the number of genes
(ignorning HIV and Mycoplasma)!
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Genomes terms genome projects species
differences extranuclear DNA
Non-coding DNA
The of the genome that is coding has a huge
variation!
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Genomes terms genome projects species
differences extranuclear DNA
The of the genome that is coding has a huge
variation!
An analogy using text
Compact genome XRTHISISGENEAUIXMNTHISISGENEBMMMMZ
METUTHISISGENECNB
Large genome XRHJCUNYHTRPKLSJTHISISGENEAUIXXVXVXV
XVHYTINHBGTMHBYMTIDIDJMNTHISISGENEBMMMMZNMENENGUHT
TTMNUTHEISMMM METUTHISISGENECNBUUNYBLIHIUBWERJBOUW
EJBRPJBEUBNEM
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Genomes terms genome projects species
differences extranuclear DNA
Total number of chromosomes/somatic (body) cell
Dog
78
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Genomes terms genome projects species
differences extranuclear DNA
Smallest number of chromosomes known in a
eukaryote 1 pair (2 total per somatic cell)
Myrmecia pilosula
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Genomes terms genome projects species
differences extranuclear DNA
Largest number of chromosomes known in a
eukaryote 630 pairs (1260 total per somatic cell)
Ophioglossum reticulatum, a fern
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Genomes terms genome projects species
differences extranuclear DNA
Human mtDNA 37 genes, 0.016 megabases
There is also a mitochondrial genome
Fig. 6.17
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Genomes terms genome projects species
differences extranuclear DNA
Chloroplasts have their own DNA, separate
from plant nuclear DNA
Fig. 6.18
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Learning goals Lecture 6, Genetic information
Text Reading Download extra file on web site on
What you need to know about DNA. The Figures
that you should look at can be found in this
lecture file.
You need to be able to explain the following to
yourself and to me (on exams)
Genetics is a PLAN for life What is genetics
why it is important, genetic plans genetic
reality vs analogy what you need to know about
molecular genetics in this class Essential
molecular genetics An analogy DNA, base,
nucleotide, protein, amino acid, enzyme, mRNA,
transcription, translation, gene experssion
Genomes are organized differently in different
species what is a genomes, eukaryotic
prokaryotic, chromosome nuclear DNA
extranuclear DNA, genome project DNA sequencing,
bioinformatics Kilobase (kb), megabase, species
differences in genomes