PTYS 214 – Spring 2011

Homework #1 DUE in class TODAY

Homework #2: available for download from the class website DUE next Thursday, Jan. 27

Class website: http://www.lpl.arizona.edu/undergrad/classes/spring2011/Pierazzo_214/

Useful Reading: class website “Reading Material” http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.863 http://www.youtube.com/watch?v=teV62zrm2P0 http://en.wikipedia.org/wiki/Cell_(biology) http://www.cellsalive.com/cells/3dcell.htm http://www.americanscientist.org/issues/feature/the-origin-of-life/

Announcements

Quiz #1

Total Students: 27

Class Average: 3

Low: 1

High: 4

If you have questions see Lissa

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Chains of nucleotides linked together by dehydration reactions between the phosphate group of one and the sugar residue of the next

Example: RNA Bases used:

- Guanine - Cytosine - Adenine - Uracil

Polynucleotides

Deoxyribonucleic Acid (DNA)

Stores the genetic code

Two polynucleotide strands held together by hydrogen bonds between adjacent bases:

- Guanine - Cytosine - Adenine - Thymine

The two DNA strands are complementary

The two DNA strands are

complementary

Can you think of any reason for

two DNA strands?

DNA vs. RNA ?

1.Choice of sugar

2. Choice of bases

3. Structure: Double vs. single strand!

Movie: The Genetic Code

The language of DNA (RNA)DNA is a string of letters (the bases of the nucleotides)

English Language DNA Language

Letters 26, from A to Z 4: A, G, C, T(U)

Units Words (different lengths) Codons (3 “letters” )

Language Ordered succession Ordered succession of words of codons (proteins)

Each codon represents a particular amino acid

Each codon represents a particular amino acid

43= 64 “words” representing 20 amino acids plus one start and 3 end signals

Three major functions of DNA/RNA

DNA mRNA ProteinTranscription Translation

Replication

Three major functions of DNA/RNA

DNA mRNA ProteinTranscription Translation

ReplicationReplication

Replication: DNA DNA (Templated Polymerization)

Explanation of Darwin’s theory

DNA replication proceeds with high speed – human DNA (3-billion-base sequence) can be copied in several hours

Even though DNA replication proceeds with incredible accuracy, errors do occur (< 1 error per billion bases copied) – mutations

If the organism survives the mutation, it will be copied every time DNA is replicated

Mutations cause diversity within species

Some mutations have no effect, some are lethal and in very rare occasions mutations are useful – basis for evolution

Three major functions of DNA/RNA

DNA mRNA ProteinTranscription Translation

Replication

Transcription

Transcription: DNA mRNA

mRNA carries the information on how to form proteins

Like DNA replication, but only a section (gene) of one DNA strand is duplicated

mRNA messenger RNA

Three major functions of DNA/RNA

DNA mRNA ProteinTranscription Translation

Replication

Translation

Each type of tRNA can attach a specific amino acid at one end, and at its other end displays a specific sequence of three nucleotides (anticodon)

Transfer RNA (tRNA)

Translation: RNA Protein

RNA typesmRNA = messenger RNA (mRNA)

RNA molecule that transcribes a piece of DNA to specify the amino acid sequence of protein(s)

tRNA = transfer RNA (tRNA) Set of small RNA molecules used in protein synthesis as an interface (adaptor) between messenger RNA and amino acids

rRNA = ribosomal RNA (rRNA) Any one of a number of specific RNA molecules that form part of the structure of a ribosome and participate in the synthesis of proteins

DNA Laboratory

Replication Transcription Transport Translation

Where is all of this happening?

The Cell

Smallest unit of any living organism which can:a) Gather raw materials from the environmentb) Construct out of them a new cell with a new copy

of the hereditary information

Think of it as a small bag of macromolecules that is separated from the outside world by a membrane (cell wall); nucleic acids, proteins, lipids, carbohydrates are parts of the living organism but not living organisms by themselves

Common features of all Cells

All Cells store their hereditary information in the DNA

All Cells replicate their hereditary information by templated polymerization

All Cells transcribe portions of their hereditary information into the same intermediary form (RNA)

All Cells use proteins as catalysts

Cells can be very diverse but they are discriminated by whether or not they have a cell nucleus that walls off genetic material from the rest of the cell

Eukaryotic Cells have a cell nucleus

Prokaryotic Cells no cell nucleus

Cell Types

These two types of cells identify the main domains of life

ProkaryotesSingle-celled

organisms

Some have photosynthetic pigments (cyanobacteria)

Some have external whip-like flagella for locomotion or hair like pili for adhesion

Eukaryotes They may be either single-celled or

multicellular organisms

Amoeba Plant cell Animal cell

There are many different types of eukaryotic cells - Plant cells are quite different from animal cells - There are approximately 210 distinct cell types in the adult human body

Eukaryotes vs. Prokaryotes

Who came first?

Who outnumbers and outweighs the other?

Procaryotes constitute 80% to 90% of the Earth’s biomass (over 2,500 species known)

First question of Astrobiology:

“How does life begin and evolve?”

We know that: a) Life requires carbon-based macromolecules – lipids,

proteins, carbohydrates, nucleic acids

b) The smallest living units of life are cells

There are two approaches for investigating the origin of life:

“Biological” – Top-down strategy “Chemical” – Bottom-up strategy

How did life originate?

“Top-down strategy” Look at the present day biology and

extrapolate back towards the simplest living entities

“Bottom-up strategy” Make the complex building blocks of

life (organic macromolecules) and put them together

Top-down strategy

Is there a minimum requirements on the number of genes (DNA information)?

The minimum number of genes for a viable cell in today's environments is probably no less than 200–300

– Mycoplasma genitalium (parasite in mammals) has the smallest known genome of free-living organisms, with about 480 protein-coding genes and over 582,000 nucleotide pairs

– Carsonella rudii (endosymbiotic bacterium in small insects) has the smallest known genome of any li ving organisms, with 182 genes and about 160,000 nucleotide pairs (probably missing genes essential for life)

Eukaryotes appear much more complex than prokaryotes

Do we see the difference in the DNA structure?

Corresponding segments of the gene for 16S rRNA (~1500 nucleotides, coding for ribosome) for different organisms:

an archaean (Methanococcus jannaschii) a eubacterium (Escherichia coli) a eucaryote (Homo sapiens)

Sites where the nucleotides are identical between species are indicated by a vertical line

Genetic information conserved since the beginnings of life

Is the genome (order of nucleotides) of Eukaryotes and Prokaryotes completely different?

Top-down strategyThe Tree of Life

By looking at the changes in 16S rRNA we can identify three domains of life Bacteria, Archaea, and Eucaryotes

Pro

kary

otes

Single cell organisms

Single and multiple

cell organisms

Top-Down Strategy: Problems with the DNA/RNA/protein world

DNA has information to reproduce itself but needs proteins to catalyze the reaction

Proteins can catalyze reactions but cannot reproduce by themselves

It is very unlikely that all DNA/RNA/proteins components would form spontaneously at the same time

The RNA World Hypothesis

RNA is an information carrier (like DNA) RNA molecules can act as catalysts

(unlike DNA)

Partial Success: Up to 14 nucleotides have been added to a primer using RNA as template and only RNA enzymes (ribozymes)

(Johnston et al, Science 292, p.1319, 2001)

RNA worldDNA/protein

world

Two Major Problems

How can RNA-type nucleotides be produced without life?

Difficult, based on laboratory work

E.g., formation of adenosine (RNA subunit)

How do RNA-type nucleotides combine into the first RNA-type molecule that can replicate?

Dilution problem

The Metabolism-first Hypothesis

Before RNA could form simple molecules started to form simpler metabolically active entities via autocatalytic cycles

Example: the iron-sulfur world (metabolically active entities occur on the surface of pyrite, FeS)

Once a primitive metabolic cycle is established, it begins to produce ever more complex compounds

These entities eventually began to self-replicate and eventually give rise to the RNA world

Metabolic entities

RNA worldDNA/protein

world