PTYS 214 – Fall 2019

Midterm 1 graded!

Office hours: T,Th 2:30--3:30 SS 423a

Announcements

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Midterm #1

Total Students: 14

Class Average: 72

Low: 22

High: 97

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If you have questions see me!

Do your Homework and make sure you understand it!

Remember: 3 midterms are dropped!

Atoms

• Protons, electrons, neutrons; charge, mass

Chemical Bonds

• Ionic, Covalent, Hydrogen

Carbon and Polymerization

Organic vs. Inorganic Compounds

Alternatives to Carbon

Organic Molecules / Building Blocks of Life

• Lipids, Carbohydrates, Proteins, Nucleic Acids

Last Time

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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

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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

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DNA vs. RNA ?

1.Choice of sugar

2. Choice of bases

3. Structure: Double vs. single strand

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The language of DNA / RNADNA can be thought of as a string of letters (the bases of the nucleotides)‏:‏

English Language DNA Language

Letters 26: A -- Z 4: A, G, C, T(U)‏

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

Language Ordered succession Ordered succession of words of codons

What do you think this language describes?

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Each codon represents an amino acid!

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

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Three major functions of DNA/RNA

DNA mRNA ProteinTranscription Translation

Replication

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Three major functions of DNA/RNA

DNA mRNA ProteinTranscription Translation

Replication

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Replication:‏ DNA → DNA (Templated Polymerization)‏

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Note:‏ polymerase, helicase, primase are enzymes (proteins)‏!

Explanation of Darwin’s theory

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

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

Mutations cause diversity within species

Some mutations have no effect, most are detrimental, and in very rare occasions mutations are useful – basis for evolution via natural selection

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Three major functions of DNA/RNA

DNA mRNA ProteinTranscription Translation

Replication Transcription

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Transcription:‏ DNA → mRNA

mRNA carries the information on how to build proteins

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

mRNA messenger RNA

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Three major functions of DNA/RNA

DNA mRNA ProteinTranscription Translation

ReplicationTranslation

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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)‏

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Translation:‏ RNA → Protein

Note:‏ RNA can be a catalyst!

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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

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Why proteins? Proteins have the diversity to allow them to perform the various functions necessary to maintain a living organism

Structures: hairs, horns, eye lenses Molecular recognition and signaling Catalysis (enzymes)‏ Molecular transport: e.g., hemoglobin binds with O

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Mechanical actions: generate forces and torques

Replication / Protein Factory

Replication Transcription Transport Translation

Where is all of this happening?

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The Cell

Smallest unit of any living organism that can:• Gather raw materials from the environment• 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)‏

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Common features of all Cells

All Cells store their hereditary information in 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

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Cells can be very diverse but they are classified 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:

prokaryotes and eukaryotes23

ProkaryotesSingle-celled organisms

Some have photosynthetic pigments (cyanobacteria)‏

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

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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

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Eukaryotes vs. Prokaryotes

Which came first?

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How does life begin?

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 approach “Chemical” – Bottom-up approach

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“Top-down” approachLook at the present day biology and

extrapolate back towards the simplest living entities

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

life (organic macromolecules)‏ and put them together

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Top-down approach

Is there a minimum requirement for the number of genes (DNA information)?

The minimum number of genes for a viable cell in today's environments is thought to be 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 living organisms, with 182 genes and about 160,000 nucleotide pairs (probably missing genes essential for life)‏

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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

How do the genomes (order of nucleotides) of Eukaryotes and Prokaryotes compare?

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Top-down approachThe Tree of Life

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

Pro

kary

otes

Single cell organisms

Single- and multi-cell

organisms

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Problems with initiating the DNA/RNA/protein system

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

Proteins can catalyze reactions but need DNA to “reproduce”

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

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The RNA World Hypothesis

RNA is an information carrier (like DNA)‏ RNA can self-replicate RNA molecules can act as catalysts (unlike DNA)‏

DNA/protein world may have evolved from RNA world.

RNA worldDNA/protein

world

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Two Problems

How can RNA-type nucleotides be produced without life?

Difficult, based on laboratory work major problem

How do RNA-type nucleotides find each other so as to combine into the first RNA-type molecule that can replicate?

Dilution problemless major problem

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The “Metabolism”-first Hypothesis Before RNA could form, simple molecules started to form from simpler metabolically active entities via autocatalytic cycles; e.g.:

Once a primitive metabolic cycle is established, it begins to grow exponentially

These entities could be subject to a primitive form of selection, eventually giving rise to RNA

Metabolic entities

RNA worldDNA/protein

world35

A + B → 2B

C + A + B → 2B + C

Homework #4 available shortly on the web site

Homework

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Next time: Organic synthesis (bottom-up approach)!