Download Phys 214. Planets and Life - Department of Physics, Engineering

Phys 214. Planets and Life
Dr. Cristina Buzea
Department of Physics
Room 259
E-mail: [email protected]
(Please use PHYS214 in e-mail subject)
Lecture 15. DNA and heredity.
Induced pluripotent stem cells.
February 11th, 2008
Contents
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Textbook pages 165-166, 171-178
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DNA and heredity
How is heredity encoded in DNA
DNA replication
Genes and genomes
Induced pluripotent stem cells
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Classification of life
Microscopic life
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News - changes in the calendar
Quizzes: 25 February, 10 March, 24 March
Assignments - 3 March, 17 March
(Note that I removed an assignment).
DNA and heredity
All life on Earth encode hereditary info in DNA &
RNA (some viruses).
DNA (Deoxyribonucleic acid) double helix = 2
phosphate deoxyribose backbones
RNA (Ribonucleic acid) a single strand – a single
backbone of ribose – bases exposed
The basic molecular building blocks of DNA and
RNA are the bases - nucleotides.
Of the many possible nucleotides, the DNA used in
living organisms on Earth uses only four.
The four DNA bases:
A - adenine, G - guanine, T - thymine, C - cytosine
The only possible pairing between bases:
A-T, and C-G
Instead of thymine, RNA uses the nucleotide base
uracil.
RNA is very important – carries out genetic
instructions – messenger RNA (mRNA), transfer
RNA (tRNA) collects amino acids, ribosomal
RNA (rRNA) building proteins in ribosomes.
How is heredity encoded in the DNA
DNA determines the structure and function of
the cells.
The operating instructions are contained in the
arrangement of bases (A,T,C,G).
Gene = the instructions that represent an
individual function (e.g. how to build a
protein).
Gene - long strand of DNA that contains:
1) a promoter (controls the activity of a gene),
and
2) coding sequence (determines what the gene
produces) exon
3) non-coding sequence - intron (can regulate
the conditions of gene expression {process
in which the information encoded in a gene
is converted into a form useful for the
cell.}).
Genome = the complete set of genetic
information that makes up an organism.
http://publications.nigms.nih.gov/moleculestomeds/images/newtcells
Chromosome
National Institute of Health
Cell stained with flourescent dyes
undergoing chromosome duplication.
The material stained red is the cell
membrane, light blue - chromosomes.
How is heredity encoded in the DNA
The genetic code. 3 DNA bases
in a row and four to choose from
= 43 = 64 larger than the 20
amino acids used to built
proteins (20) – redundant
ACC and ACA represent the
same amino acid
The codes for many amino acids
depend on the first 2 bases of the
three (probably early life used a
two-base language.
A strand of DNA has a long unbroken sequence of bases: e.g. ACTCATTCAAGC.
Set of rules of how to read the sequence – break in words, where to start and stop.
Genetic code = set of rules for reading DNA = the same in nearly all living organisms
on Earth.
Genetic words consist of three DNA bases in a row; For protein building each word is
either a particular amino acid or a “start” “stop reading” instruction.
How is heredity encoded in the DNA
The genetic code the same in nearly all living organisms on Earth!
Variations in the genetic code found in mitochondria – organelle in eukaryote cells that
contain their own DNA! (symbiotic relationship between microorganisms that lead to
lateral gene transfer)
Genetic code is like a language – everyone spoke the same language -> common ancestor
Mitochondrion
(up) scanning
electron
microscope
image (SEM)
(down)
transmission
electron
microscope
image (TEM)
DNA replication
DNA is copied via a process called replication.
(1) DNA double helix -> (2) unzip -> (3) each strand serve as
template for a new strand, according to the base pairing rule ->
(4) Two identical copies of the original DNA (going to the
dividing cell)
The two strands making up the double helix of DNA are said to be
complementary (not identical).
DNA replication very fast. Three billion base sequence in human
genome – in a few hours.
How is heredity encoded in the DNA
Diagram of the "typical" eukaryotic proteincoding gene. Promoters and enhancers
determine what portions of the DNA will be
transcribed into the precursor mRNA (premRNA). The pre-mRNA is then spliced into
messenger RNA (mRNA) which is later
translated into protein.
DNA is enclosed in the cell nucleus and
never gets out. The information is sent
out by messenger RNA (mRNA).
Gene expression = process in which the information encoded in a gene is converted
into a form useful for the cell (mRNA or proteins).
1) Transcription - process of converting a sequence of nucleotides in a section of
DNA to a sequence of nucleotides in RNA, as a precursor to protein synthesis .
2) Translation - process of converting a sequence of nucleotides in messenger RNA
into a protein (in ribosomes)
Mutations and evolution
Many enzymes involved in DNA replication - errors less than one per billion base copied.
Mutation = any change in the base sequence of an organism’s DNA (attachment of the wrong
base, extra base in a gene, a base deleted, entire sequence duplicated or eliminated).
Some mutations are benign: ACC changes into ACA – code for the same amino acid = the
instructions for the same protein made by the gene
Mutations that add or delete a base within a gene have the most detrimental effect on protein
structure (no punctuation or spacing between words).
Sickle-cell disease = mutation in the gene that makes hemoglobin
Some mutations are beneficial leading to evolution.
Lateral gene transfer = transfer of genes from one
organism to another.
Bacterial resistance to antibiotics
Genetic engineering (insulin produced by bacteria
that have been inserted with human gene for insulin)
Lateral gene transfer leads to faster speciation
(appearance of a new species) than individual
mutations (later on this subject).
How is heredity encoded in the DNA
DNA is packaged in chromosomes.
Chromosomes contain:
- a single continuous piece of DNA (which
contains many genes)
- DNA-bound proteins (serve to package the DNA
and control its functions).
Chromosomes vary between different organisms:
- eukaryotic cells (with nucleus) - DNA molecule
-large linear chromosomes
- prokaryotic cells (without nucleus) - smaller
circular chromosomes (plasmid).
A scheme of a condensed (metaphase)
chromosome. (1) Chromatid - one of the two
identical parts of the chromosome after S
phase. (2) Centromere - the point where the
two chromatids touch, and where the
microtubules attach. (3) Short arm. (4) Long
arm.
How is heredity encoded in the DNA
How is heredity encoded in the DNA
Genes and genome
Eukaryotes - no clear relationship between genome sizes and
complexity.
The latest estimate in the number of genes in the human
genome - under 3 billion base pairs and about
20,000–25,000 genes [Pennisi 2007 Science 316 (5828):
1113].
Amoeba -over 670 billion base pairs (200 times > human
genome). Rice – has 37,000 genes.
Every member of a species has the same basic genome, with
some variation between individuals.
In general – every cell in a living organism contains the same
set of genes as other types of cells of the same organism.
(muscle cells, brain differ because they express or use
different portions of the full set of genes.
One cell contains the set of instructions to build an entire
organism or any type of cell.
Cloning = process by which a single cell from a living
organism is used to grow an entirely new organism with
an identical set of genes.
Amoeba
http://www.dr-ralf-wagner.de/
Storing operating instructions
is essential for life to exist!
Extraterrestrial life may not
use DNA to store
information but will very
likely use a molecule with
a similar function.
Induced pluripotent stem cells
Every cell in a living organism contains the same set of genes as other types of cells
of the same organism!
Example: induced pluripotent stem cells
how our genetic material expressed in all of our adult somatic cells (any cells forming
the body of an organism, as opposed to germline cells) can be utilized to generate any other
tissue or treat disease.
Stem cells = retain the ability to renew themselves and can differentiate into a wide
range of specialized cell types (brain, muscles, etc).
Embryonic stem cells (ES) - found in blastocysts (embryo)
There is a great deal of controversy in our scientific
community in how should research on embryonic
stem cell research should be directed.
There is not only lack of consensus on how to
pursue scientific questions using ES cells, lack of
funding from governments, but also, lack of clear
laws given the ethical dilemma that ES cells use
implies.
Induced pluripotent stem cells
After Shinya Yamanaka from Kyoto University first demonstrated that he could
reprogram adult somatic cells in something that look like an embryonic stem cell, a surge
of disbelief and awe was followed by an incredible interest into finding what Shinya
called induced Pluripotent Stem cells or iPS.
Pluripotent = ability to develop into multiple cell types including nervous system, skin,
muscle, and skeleton.
Induced pluripotent stem cells
Enucleated
= A cell
with its
nucleus
removed
Embryonic
Stem Cells
Hallmark of
ES cell
programming
(embryo)
Induced
Pluripotent
Stem Cells
Induced pluripotent stem cells
Yamanaka’s group was the first to demonstrate that a handful of genes, namely, Oct3/4,
Sox2, c-Myc, and Klf4 (Takahashi and Yamanaka, Cell 2007) were required to re-program
mouse embryonic fibroblast (MEF) and adult mouse tail-tip fibroblast to what they called
induced Pluripotent Stem cells (iPS).
iPS generated were indistinguishable from Embryonic Stem cells (ES) in morphology,
proliferation, gene expression and the ability to give rise to teratoma formation (tumor
consisting of different types of tissue). Teratoma formation is a proof of principle towards
demonstrating that any somatic adult cell can become, upon the re-expression of the right
genes, pluripotent.
Induced pluripotent stem cells
Induced pluripotent stem cells
Fibroblast
iPS
Induced pluripotent stem cells
Induced pluripotent stem cells
Derivation of autologous (self) iPS cells from h!S/h!S
mice and correction of the sickle allele by gene
targeting
Induced pluripotent stem cells
Classification of life
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Old classification - two kingdoms - plants & animals
Main difference between plant and animal cells: plant cells have a cell wall that
helps protect the cell membrane, while animal cells do not.
This classification does not work for microorganisms.
Modern classification based on cell biochemistry, including genetics.
Microscopic life
From a microscopic structural point
of view, cells on Earth come in
two types:
1. Without a nucleus - prokaryotes.
2. With a nucleus - eukaryotes.
Cell nucleus - an internal membrane
that effectively walls off the
genetic material (DNA) from the
rest of the cell.
All prokaryotes are unicellular
(bacteria).
Eukaryotes can be:
- unicellular (amoeba)
- or multicellular (humans, plants,
animals).
All multicellular organisms are
eukaryotes.
E. Coli
Microscopic life - the dominant form of life on Earth
Much of microscopic life is harmful: E. Coli,
Salmonella (food poisoning), Chlamydia
pneumonia (heart disease, Alzheimer’s disease),
Helicobacter pylori (gastric ulcer ), nanobacteria
(kidney stones), streptococcal bacteria (pediatric
obsessive-compulsive disorder) C. Buzea et al.
Helicobacter Pylori
Biointerphases 2 (2007) MR17
Not all bacteria are harmful, some are crucial for our
survival.
- intestinal bacteria provide vitamins
- cycling carbon (decomposing) organic matter, soil,
and atmosphere
- fermentation cheese, genetic engineering, antibiotics
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Just because there are small, single-cell organisms
are not a minor form of life!
Microbes are the dominant form of life on Earth!
Total mass of microbes in the oceans is about 5,000
times larger that of all humans!
Streptomyces bacteria that produce the
antibiotic streptomycin
Next lecture
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Phylogenetic tree
Metabolism, ATP, carbon and energy sources, water