Phys 214. Planets and Life

Dr. Cristina Buzea

Department of Physics

Room 259

E-mail: cristi@physics.queensu.ca

(Please use PHYS214 in e-mail subject)

Lecture 15. DNA and heredity.

Induced pluripotent stem cells.

February 11th, 2008

Contents

• Textbook pages 165-166, 171-178

• DNA and heredity• How is heredity encoded in DNA• DNA replication• Genes and genomes• Induced pluripotent stem cells

• Classification of life• Microscopic life

• 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 = 2phosphate deoxyribose backbones

RNA (Ribonucleic acid) a single strand – a singlebackbone of ribose – bases exposed

The basic molecular building blocks of DNA andRNA are the bases - nucleotides.

Of the many possible nucleotides, the DNA used inliving organisms on Earth uses only four.

The four DNA bases:A - adenine, G - guanine, T - thymine, C - cytosineThe only possible pairing between bases:A-T, and C-GInstead of thymine, RNA uses the nucleotide base

uracil.RNA is very important – carries out genetic

instructions – messenger RNA (mRNA), transferRNA (tRNA) collects amino acids, ribosomalRNA (rRNA) building proteins in ribosomes.

How is heredity encoded in the DNA

DNA determines the structure and function ofthe cells.

The operating instructions are contained in thearrangement of bases (A,T,C,G).

Gene = the instructions that represent anindividual function (e.g. how to build aprotein).

Gene - long strand of DNA that contains:

1) a promoter (controls the activity of a gene),and

2) coding sequence (determines what the geneproduces) exon

3) non-coding sequence - intron (can regulatethe conditions of gene expression {processin which the information encoded in a geneis converted into a form useful for thecell.}).

Genome = the complete set of geneticinformation that makes up an organism.

Chromosome

National Institute of Health

http://publications.nigms.nih.gov/moleculestomeds/images/newtcells

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

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.

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.

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 astemplate for a new strand, according to the base pairing rule ->(4) Two identical copies of the original DNA (going to thedividing cell)

The two strands making up the double helix of DNA are said to becomplementary (not identical).

DNA replication very fast. Three billion base sequence in humangenome – in a few hours.

How is heredity encoded in the DNA

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)

Diagram of the "typical" eukaryotic protein-

coding gene. Promoters and enhancers

determine what portions of the DNA will be

transcribed into the precursor mRNA (pre-

mRNA). 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).

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 wrongbase, 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 = theinstructions for the same protein made by the gene

Mutations that add or delete a base within a gene have the most detrimental effect on proteinstructure (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 (whichcontains many genes)

- DNA-bound proteins (serve to package the DNAand control its functions).

Chromosomes vary between different organisms:

- eukaryotic cells (with nucleus) - DNA molecule-large linear chromosomes

- prokaryotic cells (without nucleus) - smallercircular 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 andcomplexity.

The latest estimate in the number of genes in the humangenome - under 3 billion base pairs and about20,000–25,000 genes [Pennisi 2007 Science 316 (5828):1113].

Amoeba -over 670 billion base pairs (200 times > humangenome). Rice – has 37,000 genes.

Every member of a species has the same basic genome, withsome variation between individuals.

In general – every cell in a living organism contains the sameset of genes as other types of cells of the same organism.(muscle cells, brain differ because they express or usedifferent portions of the full set of genes.

One cell contains the set of instructions to build an entireorganism or any type of cell.

Cloning = process by which a single cell from a livingorganism is used to grow an entirely new organism withan 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

Hallmark of

ES cell

programming

Embryonic

Stem Cells

Induced

Pluripotent

Stem Cells

Enucleated= A cellwith itsnucleusremoved

(embryo)

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

• 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), Chlamydiapneumonia (heart disease, Alzheimer’s disease),Helicobacter pylori (gastric ulcer ), nanobacteria(kidney stones), streptococcal bacteria (pediatricobsessive-compulsive disorder) C. Buzea et al.

Biointerphases 2 (2007) MR17

Not all bacteria are harmful, some are crucial for oursurvival.

- intestinal bacteria provide vitamins

- cycling carbon (decomposing) organic matter, soil,and atmosphere

- fermentation cheese, genetic engineering, antibiotics

• Just because there are small, single-cell organismsare not a minor form of life!

Microbes are the dominant form of life on Earth!

Total mass of microbes in the oceans is about 5,000times larger that of all humans!

Streptomyces bacteria that produce the

antibiotic streptomycin

Helicobacter Pylori

Next lecture

• Phylogenetic tree

• Metabolism, ATP, carbon and energy sources, water