Asking About Asking About LifeLife

Chapter 1 & 2Chapter 1 & 2The Scientific MethodThe Scientific Method

andandThe Chemical The Chemical

Foundations of LifeFoundations of Life

Scientists use the scientific method. The first 2 steps are observation and asking a question. Scientists make a hypothesis that you can devise an experiment to prove or disprove.

A good experiment tests a hypothesis under controlled conditions . A control is a duplicate experiment in which everything is the same except the experimental variable.

Collect data- It must be quantitative, measure something (weight) to draw a conclusion.

Draw conclusion – Accept or reject a hypothesis according to a statistical standard you set before the experiment.

A theory is a group of statements that explain facts that hold up to repeated testing.

All organisms are alike in 8ways:a) Consist of parts

b) Made of cellsc) Perform chemical reactionsd) Obtain energy from surroundingse) Respond to environment

f) Mature (grow)g) Reproduceh) Share common evolution.

Organisms self-regulate by:

1.Barrier to the outside world.

2.Homeostasis

Cells can be:

1.Eukaryotes- contain a nucleus and have many organelles. 2.Prokaryotes – no nucleus or organelles. Eukaryotes evolved from prokaryotes.

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Evolution occurred in the last 4.5 billion years. Biologists now divide organisms into 3 domains:1.Archea – bacteria.(ancient to present) 2.Eubacteria – bacteria.(more recent to present)3.Eukarya- 4 kingdoms , Plantae, Animalia, Fungi, and Protista.

1.4 million kinds of organisms are identified. Biologists believe that most species have yet to be discovered. More species have become extinct than live now.

Photo taken at S.Dakota Museum of Natural History

Members of species are similar because they have inherited similar genes made of DNA . Human DNA contains about 42,000 genes, a set of genes is a genome.

Species differ in adaptations to distinct environments which are inherited, they increase the chance an individual will live and reproduceAdaptations are size, form, color, internal structure, and chemical properties.

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Life is diverse because diversity of habitats favors organisms with different adaptations.Structure is related to function.

Diversity of life resulted from evolution.

Charles Darwin published “On the Origin of Species” in 1859. He proposed a way in which evolution could work. He modeled his idea of how evolution worked on “selective breeding” of farmers.

EX. Seeds from strong wheat plants were used to produce the next years crop.

Darwin saw a similar kind of selection operate in nature and called it “natural selection”.

Natural selection depends on the organisms environment. Darwin thought this was how organisms gradually evolved.

Geyser – yellow color due to archebacteria that live there.

Experimental Design- Biologists use a lot of individuals. How many should be used? Using only 10 individuals is not conclusive because 10 can vary a lot. The greater the variation the more individuals are needed. By using statistics variation can be estimated by small experimental groups.

Statistics is the mathematics of collecting and analyzing numerical data. It has 2 uses:

1.Estimate the actual (true) probability of something.

2.Help test a hypothesis.

Statistics can measure the probability that what we measure is real, not a random effect.

Data in tables, graphs, and other pictures can suggest new hypotheses.

Statistics states an assumption clearly.

EX. In a study of heart attack rates in men, although the study refers to all men, only a sample of men are studied.

The best way to do the study is by a random sample. Choose the sample irregardless of race, diet, and other variables. Of a population of 100 men choose a sample of 25 randomly. If 33 of the population eventually have a heart attack how many of the sample population had heart attacks?(8)

Flipping a coin 100x gets an average of 50H : 50T. In 10 flips it is unlikely to get 5H :5T. Random effects are big in small samples and small in big samples.

How do scientists estimate a value? The mean is the average. A second measure is standard deviation, an estimate of variation in the total population (not just the sample).

How can biologists tell if 2 groups differ?

If a sample size is too small, the sample mean differs from the population mean.

You can estimate variation in data. How much individual variation exists is shown by how far is each data point from the mean. The average of these distances is the standard deviation.

Ex. Average length of worms. a = 3 cm., b = 5cm., c = 7cm.

Mean = 5 cm.

To calculate Standard Deviation:

Measure the variation, square the variation, sum the squares, divide by the total number of data points minus 1 (degrees of freedom) and take the square root.

Example Calculation of Standard Deviation3 – 5 = (-2) squared = 4, 5 – 5 = 0 squared = 0, 7 – 5 = 2 squared = 4.The square root of 8/2 = 2. If the sample size is larger the true standard deviation is smaller.

If the 3 worms were 5.1 cm, 5.0 cm., and 4.9 cm. the standard deviation would be the square root of [(0.1) squared + (0.0) squared + (-0.1) squared divided by 2] = the square root of 0.2.

This standard deviation shows less variation and is more confident that 5 is the true mean. If variation is large your sample size is too small, Knowing standard deviation is important but only accurate if numbers are distributed normally around the mean (bell curve) with an equal number of data points to each side of the mean.

When data have a normal distribution, 68% of data points fall within 1 S.D., 95% will fall within 2 S.D. (P.16). In a normal distribution if you know the mean and S.D. of 2 samples you can calculate the probability that the mean of the experimental group is different from the controls.

The Chemical Foundations (Chapter 2)

Matter occupies space and has mass. There are 92 naturally occurring elements made of atoms composed of neutrons, protons, and electrons.

A molecule is a stable combination of 2 or more atoms. EX: O2. Most molecules are compounds, pure substances formed from 2 or more different elements. EX: H2O. Properties of compounds differ from those of atoms that make them up.

Compounds are described by formulas, CH4 is methane. Most matter is a mixture of compounds. Components of mixtures can be present in any ratio.

Until the 16th C. chemistry’s beginnings were alchemists trying to turn lead to gold.

In the 19th C. chemistry began to develop. Biologists use chemistry to learn biology on a molecular level, Ex: effect of NO, or Ca ++ in muscle contraction. Matter of non-living things is unlike matter of living things.

2 traits of living matter distinguish it:

1. Organization of the nucleus.

2. Limited number of kinds of molecules that make it up. (contain carbon).

By the 19th C. chemists could distinguish elements from compounds by their properties. The way a substance breaks down is due to its structure. John Dalton said elements were made of atoms.

Each element has a characteristic mass. C weighs 12x an atom of H. Weight is the effect of gravity on mass. The mass of every kind of atom is nearly a multiple of the mass of the H atom.

This suggests an atom of C is composed of 12 particles, each about the size of one H atom or 1 “dalton”. O is 16 daltons. H2O is 18 daltons.

The internal structure of an atom is mostly space. In 1910 Ernest Rutherford bombarded gold foil with positively charged alpha particles produced by decay of radium. He determined most of the mass of the atom was the nucleus.

The nucleus is about 1/10,000 of the mass of the entire atom, and is made up of neutrons and protons. Electrons revolve around the nucleus on random paths called energy shells.

The mass of the atom is determined by the protons and neutrons. If an atom has a different number of neutrons than the most stable form it is an isotope. Carbon -12 is stable. Carbon-14 is radioactive. Its nucleus has 6 protons, and 8 neutrons.

Every 4 seconds, 4 C-14 atoms in a trillion turn into Nitrogen because one of the neutrons decomposes into a proton and an electron (beta particle) which leaves the nucleus and begins to orbit. Isotopes that release beta or other particles are radioisotopes.

The time required for half of the atoms of a radioisotope to decay is its half-life. For Carbon-14 it is 5,710 years. For Uranium – 235 it is 704 million years.

An atom is most stable when it contains 8 electrons in its outer energy orbital. Inert gases already have this and are chemically inert. Most atoms have a different number so they share electrons by covalent bonds.

Covalent bonds have fixed lengths and directions. Bond lengths and angles are constant so every molecule has a definite size and shape. A water molecule always has a angled shape.

Ionic bonds are formed when atoms gain or lose electrons. Atoms take on + or – charges depending if they gain (-) or lose (+) electrons. The + and - charged atoms are held together by their opposite attraction.

Na (1 e- in the outer shell) reacts easily with Cl (7 e- in the outer shell). The atoms become Na+Cl-. This type of reaction is called electrostatic (like your hair in the winter).

Atoms of each element have a characteristic electronegativity (tendency to attract electrons). O and Cl strongly attract electrons , Na, K, and Li are least electronegative and tend to lose electrons. C has no tendency to gain or lose.

The larger the difference in electronegativity of 2 atoms the more likely to form an ionic, not covalent bond. C and N form covalent bonds. In covalent bonds atoms may not share electrons equally. The cloud of shared electrons will be closer to one atom than the other.

In water the shared electrons are more toward the O than the H’s. This causes an uneven distribution of electrical charges and water is said to be polar. When polar molecules are close to other polar molecules the – side of one is attracted to the + side of the other.

Covalent and ionic bonds are strong and take a lot of energy to break. Most chemical reactions in living organisms take place in water, different weak interactions bind molecules together. Alcohol is polar and mixes easily with water. Oil is non-polar and separates.

Water makes up 70% of organisms. Cells are bathed in water and contain water. Water molecules form crystals as they freeze and they take up more room than liquid water. Ice is less dense so it floats.

Because ice floats ponds freeze from the top down allowing fish to survive the winter at the bottom.

Given additional heat water temperature raises more slowly than other chemicals which is referred to as high heat capacity.

Water helps keep our body temperature within a narrow range that biochemical reactions need. Attraction between molecules of water is called cohesion. Cohesion produces a high surface tension that you feel with a “belly flop”.

Water is cohesive because of weak hydrogen bonds formed between two polar molecules. When an H atom attaches to an electronegative atom like O the bond is polar covalent. The H end is sort of +, the O end is sort of -. Hydrogen bonds play an important role in holding together DNA strands and bonds in proteins.

Clinging of water molecules to other material is called adhesion . Water’s adhesion results from its tendency to form H bonds with other polar molecules. Paper is made of the polar molecule cellulose which absorbs water well. Oil (nonpolar) is absorbed poorly by paper.

Because of water’s cohesive and adhesive properties it moves up a tube easily by capillary action. This is important to get water from roots to leaves in the small tubes inside of plants.

Water dissolves ionic salt and polar sugar easily. These substances do not dissolve easily in non-polar oil. Some substances have hydrophobic and hydrophilic ends and are referred to as amphipathic. The hydrophobic end repels water and hydrophilic end attracts water.

Dish soaps do this as well as the phospholipid cell membranes. The hydrophilic ends point outward and hydrophobic tails point inward. In a water solution electrons stay closer to the O than to the H. An H atom may have no electron at all and become a naked nucleus (H+).

Then the naked H+ can jump to another water molecule producing H3O+ (hydronium ion) and leaving behind an OH- (hydroxide ion). These charged ions recombine readily to re-form regular water. A molecule that gives up and H+ is a base. One that accepts an H+ is an acid.

Vinegar has more H+ ions than OH- ions so it’s an acid. Stomach acid contains a trillion x more H+ ions than OH- ions. pH is based on the logarithm of the concentration of H ions. Stomach acid has a pH = 1. Saliva has a pH = 7 (neutral).

Blood pH = 7.4 (slightly basic). If blood pH decreases to 6.95 (diabetes) the nervous system fails. Coma and death can result. If pH increases to 7.7 the nerves overreact causing muscle spasms and convulsions. Diseases, injury, and drugs (diuretics) can cause this

Small changes in pH are normal. In sea urchins sperm is immobile in testes at 7.2 but sea water has a pH of 8.0 which activates them to swim to an egg.