The Chemical Context of Life

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A Chemical Connection to Biology

Ex. Ants maintain Duroia hirsuta “devil’s gardens,” in Peru by injecting formic acid into other plants

Ants Myrmelachista schumanniThis plant is the only species in this tropical rain forest!

HCO2H.Methanoic acid

Formic acid stinging ants

Some beekeepers use formic acid as a fumigant to kill a mite which attacks the bees.

Most ant species probably use it as a disinfectant

 decalcifier; reducer in dyeing for wool; dehairing and plumping hides; tanning; electroplating; coagulating rubber latex; silage and grain preservation; solvents of perfume; lacquers;  

Scientific method• Two saplings of a common Amazonian tree, Cedrela odorata, or Spanish

cedar, were planted inside each Devil’s garden near the base of a D. hirsuta tree actively patrolled by worker ants. A sticky insect barrier was applied to one cedar sapling to exclude ants, while the other sapling was left untreated.

• The results were immediate. Worker ants promptly attacked the untreated saplings by injecting formic acid into the leaves, which began to die within 24 hours. "Most of the leaves on these saplings were lost within five days, and the proportion lost was significantly higher than on ant-excluded saplings,". Cedars treated with the insect barrier fared lived.

• Independent variable = • Control group =• Controlled variables =• Dependent variable =

Matter, elements, and compounds

• matter - anything that takes up space and has mass

• Matter is made up of elements

• element - substance that cannot be broken down to other substances

25 are essential for life in humans 94 elements occur naturally

Na Cl NaCl

Sodium and water

compound -consists of 2 or more elements in fixed ratio-characteristics different from those of its elements

http://youtu.be/m55kgyApYrY

Essential Elements of LifeAbout 25 of the 92 elements are essential to life

(humans)

• CHON =96% of living matter

• Also…….

• Trace elements required by an organism in minute quantities

(b) Iodine deficiency

Trace amounts of iodine required for thyroid function

Copper deficiency prevents full opening of leaves

An element’s propertiesdepend on structure of its atoms

• atom =smallest unit of matter that still retains properties of element

• subatomic particles• Neutrons (no electrical charge)• Protons (+ charge)

– # protons defines the element

• Electrons (- charge)

Isotopes

• Isotopes – Atoms of an element that differ in # of neutrons

• Radioactive isotopes – Isotope decays particles and energydecay– Half life = lifetime for ½ of the isotopes to decay

FYI

number of protons and neutrons

number of protons

12Cis stable , 6 neutrons 14C is radioactive, 8 neutrons98.89% of carbon

FYI• Atomic numbers (# protons) 1 through 40 are considered stable isotopes• Elements 41 through 82 are stable. The half lives of elements 41 through 82 are so long

that their radioactive decay has yet to be detected by experiment (100 million times longer than the age of the universe)

• 83 through 94 radioactive decay can be detected. – uranium has one or more isotopes with half lives long enough to survive as remnants of the explosive big

bang

• 94 and higher only observed experimentally – extremely short half life• Tritium (3H) low energy beta particle. 12.35 years. Used to tag DNA. No shield necessary.

Wear gloves.• Carbon-14 decays into nitrogen-14 by emission of a beta particle. Half life 5730 years. No

shield, wear gloves, can penetrate skin. • Phosphorus-32 a beta particle. Half life 14.2 days. Use plexiglass. • Iodine-125 gamma rays. 60 day half life. biological assays, nuclear medicine imaging and

in radiation therapy. Thyroid cancer treatment. Use lead shield.• Polonium has 26 isotopes, all radioactive. 250 billion times more toxic than hydrocyanic

acid. It is readily soluble in weak acid. It was the first element discovered by Marie Curie, in 1898, and named after her native Poland. Her daughter Irene was contaminated with polonium in a laboratory accident and died of leukemia at the age of 59.

FYI• 2006, Litvinenko fell ill. Earlier he had met two former KGB officers in London. Had to

do with information on death of journalist killed at her Moscow apartment 2006. • For several days , Litvinenko experienced severe diarrhea and vomiting. Litvinenko's

condition worsened as doctors searched for what caused the illness. Litvinenko began to become physically weak, and spent periods unconscious

• Shortly after death, it was found Litvinenko had significant amounts of (210Po) in his body. The poison was in Litvinenko's tea cup.

• Polonium was identified after Litvinenko's death, on 23 November. Doctors could not detect polonium earlier because it only emits alpha particles that do not penetrate human skin, thus being invisible to hospital radiation detectors . An alpha-emitting substance can cause significant damage only if ingested or inhaled, acting on living cells like a short-range weapon.

• The symptoms seen in Litvinenko appeared consistent with an administered activity of approximately (50 mCi which corresponds to about 10 micrograms of 210Po. 200 times the lethal dose

• radioactive isotopes in biology: – Dating fossils– Medical imaging– Lab research

A PET scan (positron emission tomography) detects locations of intense chemical activity. Inject patient with radioactive glucose. A scanner measures collisions of the radioactive glucose with active cells to locate tumor

Radiolabeled glucose atom used in PET scans

Example: Use of isotopes in research

Hypothesis:Cells reproduce faster at higher temperatures

Hela cells

3H-thymidine,building block of DNA

Cells

Isolated DNA is radioactive

Add tritiated thymidine to cells. Cells incorporate isotope into new DNA

1 cells at 10oC215oC320oC425oC530oC635oC740oC845oC950oC

1 2 3

7 8

9

TECHNIQUE

The test tubes are placed in a scintillation counter.

3

Measure radioactivity in counter

RESULTS

0

Results

• Structural formula represents atom bonding

H–OH

• Molecular formula abbreviation

H2O

Chemical Formulas

Chemical Bonds

1. Covalent bond – electrons shared by 2 atoms

• Ex. O2, H2O• Strong bond

2. Ionic bond – one atom loses an electron

–Ion is a charged atomNa+

Cl-

– Weaker bond– Salts

3. Hydrogen Bonds

• H atom covalently bonded to electronegative atom is attracted to another atom

4. Van der Waals Interactions

• Between molecules of the same substance • Similar to hydrogen bonds but weaker• BBC gecko • Van der waals gecko and synthetic glue

Molecular Shape and Function

• molecules have specificity/function based on shape

• similar shapes can have similar biological effects

(a) Structures of endorphin and morphine

(b) Binding to endorphin receptors

Naturalendorphin

Endorphinreceptors

Morphine

Brain cell

Morphine

Natural endorphin

Key Carbo

nHydrogen

NitrogenSulfurOxygen

Chemical reactions

Chemical reactions make and break chemical bonds– reactants - starting molecules– products - final molecules

Photosynthesis6 CO2 + 6 H20 → C6H12O6 + 6 O2light

• Chemical reactions are reversible

• Chemical equilibrium =when forward and reverse reaction rates are equal (in a closed system)