Log Scale Overview


Choosing the proper scale to use on each axis is important to get the most out of using charts to visualize data. You need to know when to use Linear, Semi-Log, or Log-Log charts when creating charts.

Palindromic Sequences

Restriction enzymes cut double-stranded DNA* at specific locations based the pattern of bases found at those locations. These enzymes predictably cut both strands because the sequences they recognize are palindromic. That is the recognition sequences are short string of identical bases on both DNA strands.

Palindromic sequences are similar to language palindromes, but follow a distinct set of rules. Any string of bases can be made into a palindromic sequence by following these rules.

Restriction Enzymes

Restriction enzymes cut DNA* at specific sites based on the sequence of bases along the strand at the cut site. These enzymes were first identified and studied in strains of the bacteria E. Coli in the 1950’s and 60’s. The term restriction was used to describe them because their activity restricted the growth of viruses that infect E. coli.

Restriction enzymes are nucleases - enzymes that cut nucleic acid polymers (i.e. DNA and RNA). There are two types of nuclease: endonuclease and exonuclease. Endonucleases make cuts within a DNA polymer. Exonucleases remove individual nucleotides* from the end of a strand. Restriction enzymes are a type of endonuclease - they cut at specific sites in the middle of DNA strands.

Gel Electrophoresis Overview

Electrophoresis is the movement of charged particles through an electrical field. Since the sugar-phosphate backbone of DNA

Meselson–Stahl Experiment

In their second paper on the structure of DNA*, Watson and Crick (pdf) described how DNA's structure suggests a pattern for replication:

"…prior to duplication the hydrogen bonds are broken, and the two chains unwind and separate. Each chain then acts as a template for the formation onto itself of a new companion chain, so that eventually we shall have two pairs of chains, where we only had one before." - Watson and Crick, 1953

This is called semiconservative replication.

Today we know that this is the pattern used by living cells, but the experimental evidence in support of semiconservative replication was not published until 1958. In the 5 years between Watson and Crick's suggestion and the definitive experiment, semiconservative replication was controversial and other patterns were considered.

DNA Polymerase

DNA polymerases are the enzymes that replicate DNA in living cells. They do this by adding individual nucleotides to the 3-prime hydroxl group of a strand of DNA. The process uses a complementary, single strand of DNA as a template.

The energy required to drive the reaction comes from cutting high energy phosphate bonds on the nucleotide-triphosphate's used as the source of the nucleotides needed in the reaction.

Refraction in lenses

When a ray of light passes through a transparent object such as a block of glass, it refracts twice. Once when it enters the glass and once again when it exits. In order to trace the complete path a ray of light takes, both these points of refraction need to be considered separately.

Drift and Selection

The Hardy-Weinberg equation describes allele frequencies in populations. It predicts the future genetic structure of a population the way that Punnett Squares predict the results of an individual cross. The equation calculates allele frequencies in non-evolving populations. It is based on the observation that in the absence of evolution, allele frequencies in large randomly breeding populations remain stable from generation to generation.

Serial Dilution

Many procedures performed in modern biology and chemistry laboratories require sets of solutions that cover a range of concentration*s. These include quantifying the number of bacteria in a sample using plate counts and development of standard curves for quantitative colorimetric, radiometric and enzymatic assays.

Bohr Atom

The Bohr model of the atom, developed in the early twentieth century, was an attempt to explain observations about the way atoms and electrons absorb, retain and release energy.

Nucleotides in RNA

Ribonucleic acids, also called RNA, perform multiple important roles in living cells. RNA is needed for protein synthesis and DNA

Lunar and Solar Tides

Tides cause daily changes in water level in many coastal areas. Factors such as local topography and weather contribute to the timing and height of tides, but the primary reason for tides is the gravitational attraction between liquid water on the Earth and the Moon. All objects on Earth experience tidal forces. However, the effect is most pronounced with water because, as a liquid, it is more easily deformed by gravity when compared to solid objects.

Genotype and Phenotype Probabilities

Patterns of genetic inheritance obey the laws of probability. In a monohybrid cross, where the allele*s present in both parents are known, each genotype* shown in a Punnett Square* is equally likely to occur. Since there are four boxes in the square, every offspring produced has a one in four, or 25%, chance of having one of the genotypes shown.

Nucleotides in DNA

The study of modern genetics depends on an understanding of the physical and chemical characteristics of DNA. Some of the most fundamental properties of DNA emerge from the characteristics of its four basic building blocks, called nucleotides. Knowing the composition of nucleotides and the differences between the four nucleotides that make up DNA is central to understanding DNA’s role in living systems.


The energy that warms Earth’s lower atmosphere comes from the Sun, but sunlight does not warm the lower atmosphere directly. This region of the atmosphere warms from below. Most of the short wavelength, electromagnetic energy from the Sun passes through the atmosphere and is absorbed by the Earth, which warms up as a result. As the Earth warms, it emits some long-wave radiation back out, heating up the lower atmosphere above it. Eventually, this energy radiates from the atmosphere back into space.

The Earth does not absorb all of the electromagnetic energy that hits it. Some reflects back out into space. This is important for the Earth’s energy balance, because only absorbed energy contributes to the temperature of the Earth/atmosphere system. The proportion of the total energy reflected by the Earth (or any object) is called the Albedo.

Punnett Square

During sexual reproduction, a parent is equally likely to pass on to its offspring either of the two alleles it has at each genetic locus. This makes it possible to list and estimate the probability of specific genotypes being produced from the pairing of two individuals. Given two allele from each parent, four allele combinations are possible. These combinations and their probabilities can be readily visualized using a Punnett square.

Features of a wave

A standard set of terminology is used to describe the feature of waves.

Wave Interference

Anyone who as watched the surface of a swimming pool has observed wave

Balancing Chemical Equations

In chemical reactions, sets of compounds interact with each other to form new compounds. Chemists use equations to describe these interactions. Like mathematical equations, chemical equations conform to a set of rules. This allows equations to provide detailed information about a reaction.

Covalent Bond Energy

Eating, putting gas in a car and throwing a log on a campfire all involve adding energy to a system. In each case, the energy is added in the form of covalent bond*s that hold atoms together in molecules.

Boyle's Law

On Earth, matter exists in one of three states: solid, liquid or gas. Matter in each state exhibits distinct characteristics. Gases, for example, do not have a fixed volume* or shape.

Light Reflection and Refraction

Light is a complex phenomena. It exhibits both wave

Specular vs Diffuse Reflection

Our ability to see and make sense of the world with our eyes depends on the reflective properties of light. Without reflection, we would only be able to see luminous objects like the sun, light bulbs and computer screens.

Pendulum Period

Clocks with quartz movements keep time more accurately than pendulum. As a result, quartz has largely replaced pendulums in modern clocks. But in their day, pendulum clocks were profoundly important. The first pendulum clocks were produced in the mid 17th century. They use ushered in a new era of accurate time keeping.

Gravitational Acceleration

We all understand that if we hold something up in the air and then let go, it will fall to the ground. Things fall because of gravity. Gravity is an attractive force between all things that have mass*.  It is one of the fundamental forces of nature. Gravity causes objects with mass to accelerate towards each other. The rate of acceleration depends on the mass of the objects and their proximity. The more mass an object contains, the more it will attract other objects. The closer an object is to another the greater the attraction between them will be.

Metric Unit Prefixes

Similar to scientific notation, unit prefixes make very large and very small number easier to manipulate and to understand.

Buoyancy II

If you wanted to move a heavy rock across the bottom of a shallow pool, would it be easier to move it if the pool was empty or full of water?

The rock would be easier to move if there was water in the pool. The reason, buoyancy force.

Scientific Notation

Some people have a strong resistance to using scientific notation*. Almost every time I teach an introductory science class, I have one or two students with good math skills who insist on doing all of their calculations in standard notation. Doing this invariably results in mistakes that lead to lost points on exams and homework.


Why do some things float and others sink? The first thing that comes to mind for many people is that it depends on how heavy an object is. While an object's weight*, or more properly its mass** does play a role, it is not the only factor. If it were, we could not explain how a giant ocean liner floats while a small pebble sinks. Mass matters, but there is more to it.

Alleles, Genotype and Phenotype

Genetics is the study of the organization, expression and transfer of heritable information. The ability for information to pass from generation to generation requires a mechanism. Living organisms use DNA. DNA is a chain, or polymer, of nucleic acids. Individual polymers of DNA can contain hundreds of millions of individual nucleic acids molecules. These long DNA strands are called chromosomes. Information is contained in the order of the individual nucleic acids that make up the DNA polymer. The use of DNA as the information molecule is a universal property of all life on Earth.

Types of Waves

Every sound we hear, every photon of light that hits our eyes, the movement of grass blown by the wind and the regular beat of the tides are all examples of wave*s. They are all around us.  Visible, physical wave*s such as those we see when a rock is thrown into water are what many people think about when they first began to think about waves. These waves have distinct properties specific to their type but also exhibit characteristics in common with more abstract waves such as sound waves and light (electromagnetic) waves.

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