a variation, or form of a gene found at specific genetic locus. Genetic variation comes from the presence of different combinations of allele*s in different individuals. Organisms contain one allele for each of their sets of chromosome*s. Diploid organisms, such as humans, have two sets of chromosomes and therefore, two alleles for each gene. An organism's genotype* is a description of the alleles present at specific genetic loci.
A chromosome involved in the determination of the sex of offspring produced via sexual reproduction. Contrast with autosomes which are not involved in sex determination. Individuals receive one allosome from each of their parents.
Humans have two types of allosomes, X-chromosomes and Y-chromosomes. Females have two X-chromosomes, and males have one X and one Y-chromosome.
Genes on the allosomes are called sex-linked genes because their inheritance and expression patterns differ between males and females.
The maximum displacement of a wave* form measured relative to the resting position of the medium through which the wave is moving. Amplitude* is measured in the orientation of particle movement. In longitudinal waves the motion is in the same orientation as energy propagation. In transverse waves, it is perpendicular to energy propagation.
Pendulums: The amplitude of pendulum is the distance between the bob's resting position and its position at maximum displacement.
- Angle of reflection
The angle formed between a reflected light ray and a line normal* to the point where the light ray hit the surface it is reflecting off of.
- Angle of refraction
A measure of the change in direction that occurs when a light ray passes through an interface between two mediums with different densities. This change in direction is called refraction*. The angle of refraction* is the angle between the transmitted light ray and a line normal* to the surface the ray transmits through. The incident angle and the difference in density* between the two media determine the angle of refraction.
One of the two types of chromosome*s present in organisms that exhibit chromosomal inheritance. Individuals receive one copy of each autosome* from each of its parent resulting in identical, matched sets of autosome regardless of gender.
Contrast with allosome*s, which differ between males and females of a species and are involved in sex determination.
- Boyle's Law
Characterizes the relationship between pressure and volume of an ideal gas. The law states that the pressure of a gas in an enclosed container is inversely proportional to the gas' volume. This means that the volume of an ideal gas will decrease as more pressure is applied. The greater the pressure applied to a fixed amount of gas, the less volume that gas will fill.
This is one of the relationships that can be derived from the idea gas laws.
The formula describing Boyle’s Law is:
Where, P1 is the pressure of a quantity of gas with a volume of V1 and P2 is the pressure of the same quantity of gas when it has a volume of V2.
The structure that hold sister chromatid*s together in eukaryotic chromosome*s. It is visible as the main constriction point on the chromosome. The centromere* is the point of attachment for the fibers that pull sister chromatids apart during mitosis.
- Charles Law
Charles' law describes the relationship between temperature and volume for ideal gases held at a constant pressure.
The law states that, under constant pressure, temperature and volume vary proportionately. Meaning, as the temperature of a gas increases, its volume also increases.
The equation for Charles' law is V1/T1 = V2/T2
V1 and T1 are volume and temperature under one condition, and V2 and T2 are volume and temperature under another set of conditions.
Behavior of real gases differs from ideal gases, but the relationship between temperature and volume and temperature for real gases is close enough to the idea case that Charles' Law can be applied to real-world cases.
The two halves of the characteristic x-shaped structure chromosome*s form during cell replication. Each chromatid* contains a complete copy of the DNA* in the chromosome. During cell division, each daughter cell gets one copy (one chromatid).
A general term used to describe the organization of DNA* in living cells. The chromosome* is considered the basic unit of DNA replication. Prokaryotic cells typically contain one (or a few) circular chromosomes. Eukaryotic cells with their much larger genomes have multiple linear chromosomes.
The length and linear nature of Eukaryotic chromosomes increases the complexity involved in storing the genetic material and passing the proper amount to each daughter cell during cell replication.
- complete dominance
The amount of solute present in a volume of water or other solvent. For chemicals, common units for concentration are weight/volume percent, weight percent and molarity.
For biologically active compounds such as antibodies or enzymes, concentrations are often reported in activity units/ml. Concentration of bacterial and cell cultures are often reported in cells / ml or colony forming units (CFU) per ml.
- covalent bond
A chemical bond between two atoms in which the atoms completely share one or more pair of electrons.
- Critical Angle
in optics, the angle of incidence between a light ray and an interface above which the ray reflects completely instead of passing through the interface from one medium to the other. The complete reflection of the light ray is referred to as total internal reflection.
The critical angle is a function of the index of refraction of the two media.
With the Snell's Law equation solved for the angle of incidence:
θi = arcsin[ sin( θr ) × nr ÷ ni ]
θr = the angle of refraction
θi = the angle of incidence
ni = the refraction idex of medium containing the incident ray
nr = the refraction idex of medium containing the transmitted ray
The critical angle is the value for θi at which θr equals 90 degrees (1.57 radians):
θi = arcsin[ sin( 90 ) × nr ÷ ni ]
Total internal reflection occurs when the θr exceeds 90 degrees (1.57 radians).
- Diffuse reflection
The type of reflection* that occurs on rough surfaces. The roughness of the surface causes light rays to scatter when they bounce off the surface. As a result, any organization present in the incident ray*s is lost. The rougher the surface, the more diffuse (scattered) the reflection.
Diffuse reflection* is essential to our ability to perceive the world with our eyes. With the exception of luminous objects such as light bulbs and the sun, everything we see depends on the diffuse reflection of light rays bouncing off of objects and into our eyes.
- diurnal tide
A tidal pattern characterized by a single tidal cycle of one high tide and one low tide every day.
The orbit of the Moon drives the tidal period*. The Moon goes around the Earth once every 24 hours and 50 minutes resulting in high and low tides occurring about an hour later each day.
Diurnal tide*s are one of the three commonly described tidal patterns. The other two common tidal patterns involve two tidal cycles per day.
an abbreviation for Deoxyribonucleic Acid, the material that carries the heritable information living organisms need to synthesis the many enzymes and proteins required for life.
- DNA Polymerase
The enzymes responsible for DNA* replication. There are different DNA polymerase*s. Each has slightly different activities. DNA replication in prokaryotes requires DNA polymerase III and DNA polymerase I. DNA polymerases do not create new polymers from scratch. They only add new nucleotides* to an existing strand using its a complementary strand as a template.
The fact that DNA polymerases can only extend existing DNA polymers using a complementary strand as a template is why DNA synthesis requires short priming sequences.
- Electromagnetic Spectrum
A term used to describe the entire range of electromagnetic radiation from long wavelength*, low frequency*, low energy radio waves on one end to short wavelength, high frequency, high energy gamma rays at the other. Visible light* covers a small range in the middle of the spectrum.
Visual depictions of the electromagnetic spectrum* are usually shown on a log scale to allow the visualization to encompass the entire range of values which, cover many, many orders of magnitude. For example, electromagnetic energy wavelengths range from 10’s to 100’s of meters for radio waves, down to femtometers for gamma rays.
- Electromagnetic wave
The movement of electromagnetic energy. Electromagnetic energy arises from interactions between electric and magnetic fields. The fact that the energy is associated with this interaction and not with disturbances in a physical medium is why electromagnetic wave*s can travel through a vacuum.
In math, a number placed above and to the right of another number indicating the number of time that number should be multiplied by itself. For example the number three with an exponent* of two, indicates that three should be multiplied by itself two times.
32 = 3 × 3 = 9
The exponent is also called the power the number is raised to. Negative exponents indicate that a number should be multiplied by one over itself which is the same as dividing.
- Genetic Drift
Changes in allele* frequency* in a population due to chance events. Genetic drift* is caused by some individuals in a population producing more offspring than others. This causes allele frequencies to diverge from the frequencies expected assuming even representation from generation to generation.
Genetic drift is an evolutionary force because it causes changes in the genetic structure of populations over time. However, the changes are not adaptive in the way that changes due to natural selection* are.
The influence of genetic drift increases as population size decreases. In relatively large populations, small random changes in allele frequencies are negligible relative to the entire population. In small populations, changes driven by genetic drift can be significant. In the extreme case, it can result in the complete loss of specific alleles from a population.
The basic unit of heredity in living things. Many individual genes specify information about specific traits such as hair color in animals or leaf shape or color in plants.
A description of the allele*s present in an organism. The term is also used to describe the set of alleles at specific genetic loci. Alleles are often distinguished from each other by case sensitive abbreviations. Dominant allele abbreviations begin with capital letters and recessive allele abbreviations begin with lower case letters.
The enzyme responsible forming the replication fork* during DNA* replication. It works by unwinding and separating the two strands of DNA that make up the double helix. The separation of the two strands is needed to allow DNA polymerase* access to the nucleotides* that make up each strand.
Helicase* is only responsible for the initial separation. Additional proteins, called helper proteins, are required to keep the replication fork open.
- Ideal Gas
A theoretical material used in physics and chemistry to describe the behaviors of gases under different conditions. In an ideal gas:
- All collisions between molecules are perfectly elastic (i.e. no energy is lost when individual molecules collide).
- Molecules remain in the gas phase all the way down to absolute zero.
- The molecules themselves have no mass or volume.
Ideal gases don’t exist, but describing ideal gases is useful because the behavior of real gases are similar to ideal gases in many real world situations.
- Incident Ray
The incoming ray of light that hits a surface in the light ray model.
- Incomplete dominance
- Loading Dye
A colored buffer mixed with a DNA* or other types of samples before loading the samples onto a gel for electrophoresis. The dye contains a relatively high concentration* of either glycerol or sucrose. This makes the dye more dense than the surrounding running buffer* and causes the sample mixed with the dye to sink into the well when placed over the well with a pipette. The loading dye* also contains a small amount of dye. Coloring the sample makes it easier to keep track of which wells contain a sample.
- Longitudinal wave
- Lunar tide
- The component of the tide caused by the gravitational attraction between the Moon and water on Earth. The Moon-Earth system rotates around its center of gravity once every 24 hours and 50 minutes. This rotational period* drives the daily tidal period on much of the planet.
The amount of matter in an object. On the earth, the weight* and mass* of an object are equivalent. However the distinction becomes important for very precise measurements or when discussing object not no the earth.
- Natural Selection
A non-random process by which some genotype*s contribute more offspring to the next generation than other genotypes. Uneven representation arises from differences in life history traits such as reproductive success or survival.
- Neap tide
The tides with the smallest tidal range during the monthly tidal cycle. They occur when the tidal bulges from the sun and the moon are not in phase. In these conditions, the gravitational force of the sun and the moon work against each other resulting is relatively small tidal ranges. They occur at the moon's quarter phases, halfway between new and full.
A line perpendicular to a surface is normal* to that surface. On a curved surface, the normal is a line perpendicular to a line tangent to the curve at a particular point.
Normals have many uses in mathematics and physics. In optics, for example, the normal line is used to calculate angels of reflection* and refraction* for light rays encountering surfaces and interfaces.
Nucleotides are synthesized from nucleoside*s by the addition of one or more phosphates to the number 5 carbon of the sugar.
In addition to their role in RNA and DNA, nucleotides participate in cellular metabolism and signaling.
The amount of time over which a wave* form repeats itself. Period* is reported in the units of seconds. The inverse of the period of a wave or other repeating cycle is its frequency* (frequency = cycles / second).
Not all genes contribute directly to distinct phenotypes, but all phenotypes are linked to a organism’s genotype. Phenotypes can be influenced by the allele*s present at more than one genetic locus as well as by environmental factors.
- Physical wave
The enzyme that initiates DNA* replication by adding a short three to ten base long RNA primer to the template strand. The priming sequence provides the 3’ hydroxyl end needed for DNA polymerase* to being synthesizing DNA.
The addition of an RNA priming sequence complicates the replication process. The RNA nucleotides* in the priming sequence need to be replaced by DNA nucleotides before the completion of replication.
In molecular biology, primers* are short lengths of single-stranded RNA (or DNA*) that attach to a longer strand of DNA to initiate DNA synthesis. This priming sequence is necessary because the DNA polymerase*s' responsible for DNA replication in living cells can’t synthesize DNA de novo. Polymerases can only extend existing strands of DNA by adding new nucleotide bases to the 3'-OH end. Primers (RNA in living cells and DNA is PCR) provide the first 3'-OH group needed for the synthesis of double-stranded DNA from a single-stranded template.
- Punnett Square
A Punnett Square* is a tool to visualize the genotype*s possible from mating a pair of individuals. It is set up by subdividing a square into enough spaces to contain every allele* combination for the gene(s) of interest given the parents genotypes.
It is most useful when looking at one or two loci because the number of possible genotypes increases rapidly as the number of loci observed increases. A single locus Punnett square contains four allele combinations. A two-locus Punnett Square contains 16 combinations, and a three locus square contains 64.
A pairing where two traits are observed is called a dihybrid cross.
Multi-locus Punnett Squares can be hard to draw and are difficult to interpret. The large number of genotypes possible with multi-locus crosses makes it easier to avoid drawing the square. Instead, the probability of specific genotypes arising are calculated using equations.
- Purine Base
A nitrogenous base that has a double ring structure made up of a five-atom ring attached by one side to a six-atom ring. The two rings contain a total of five carbon and four nitrogen atoms. Biologically significant purines include the bases adenine and guanine.
When bound to a ribose or deoxyribose sugar and a phosphate molecule, these bases form two of the five nucleotide building blocks of DNA* and RNA
- Pyrimidine Base
A nitrogenous base that has a six membered ring. The ring contains four carbon and two nitrogen atoms. Biologically significant pyrimidines include the bases thymine, cytosine and uracil.
When bound to a ribose or deoxyribose sugar and a phosphate molecule, these bases form three of the five nucleotide building blocks of DNA* and RNA.
- Real gas
Gases that behave the way molecules in the gas phase behave in the real world. The molecules in real gases have volume and mass, collisions between these molecules are not perfectly elastic and real gases have a condensation point.
Under standard temperature and pressure, far from a gas' condensation point, the behavior of real gases are similar to ideal gases. As a result, many real world situations can be explored using the idea gas laws even though real gases do not exhibit all the characteristics of ideal gases.
- Reciprocal Cross
Mating of two individuals that are true-breeding (homozygous) for different genotype*s of a trait of interest. An individual that is true-breeding for a particular trait passes the same allele* for that trait to all of its offspring.
Because true-breeding individuals always pass the same allele on to their offspring, breeding two, true breeding individuals will produce offspring that all have the same heterozygous genotype.
- Reflected Ray
In the ray model used to describe some behaviors of light, a reflected ray* is a ray of light that bounces off of an interface between two media and travels back into the original medium.
Contrast with refracted ray*, which is a ray of light that passes through the interface into the medium on the other side.
A change in direction of light or other energy wave*s when they encounter surfaces. For light rays reflecting off of a flat surface, the law of reflection* states that the angle of reflection* is equal to the angle of incidence.
Reflection is one of the three things that can occur when a light ray encounters an interface between two media. The other two things that can occur are that the energy can transmit into the new medium or be absorbed.
- Refracted Ray
In the ray model used to describe some behaviors of light, a refracted ray* is a ray that passes through an interface between two media and travels into the medium on the other side of the interface. The direction of travel of the refracted ray depends on the index of refraction* of the two media.
Contrast with reflected ray*, which is a ray of light that bounces off the surface and travels back into the original medium.
The amount a wave bends depends on the angle at which it encounters the interface. This relationship is described by Snell’s Law. The greater the angle of incidence, the larger the amount of refraction*. A wave that encounters a surface with an angle of incidence of zero does not refract.
- Replication Fork
The active region of DNA* replication where the two strands of DNA of double-stranded DNA helix are separated, and each each is used as a template to make its complimentary strand. The replication fork* is formed by the helicase* enzyme which unwinds and separates the DNA double helix to allow polymerase enzymes access to each strand for replication.
- Running Buffer
A buffered solution used in gel electrophoresis that stabilizes the environment while a gel runs. Buffering helps maintain a constant pH and provides the ions needed for electricity to flow through the gel. The running buffer* also helps keep the gel cool as the flow of current through the gel generates heat. The cooling role is especially important for agarose gels that melt if they get too hot.
- scientific notation
A convenient format for writing very small and very large numbers. The format contains a decimal fraction multiplied by ten raised to a power
- Semi-Diurnal Tide
Semi-daily tides. A term used to describe a tidal pattern characterized by two high and two low tides of roughly equal magnitude every day.
Contrast this with the mixed tidal pattern in which there are also two low and two high tides every day, but the two high and two low tides each day differ in magnitude.
- Serial Dilution
The process of reducing the concentration* of a solution by mixing small volume*s of the original solution with water (or other solvent*) over a number of uniform steps. The uniform nature of the process makes it possible to back-calculate characteristics of the original solution based on procedures performed the diluted samples.
Often 10% or less of the original sample is used in the first step of a dilution series. As a result, the diluted sub-samples can be used for a variety of procedures without consuming the bulk of the original sample.
A 10x dilution is obtained by mixing 1 part of a sample with 9 parts of a diluent so that the new solution is 10 times (10x) less concentrated than the original solution. The 10x dilution can then be diluted by a factor of 10 again by mixing it with 9 more parts of the diluent. This second step produces a 100x dilution.
Serial dilution*s are made when a sample is too concentrated for a particular procedure such as a colorimetric assay. The serial dilution process is also used to make the standard curves needed for many quantitative procedures.
- Snells Law
Describes the path light rays take when they pass through an interface between two media of different densities. It is a formal description of the way light bends when it passes through an interface between two materials with different densities. The law is derived from Snell's equation:
Θr = arcsin [ (sin (Θi) × ni ÷ nr]
The equation can be used to determine the path a light ray will take at a surface given knowledge of the densities of the two media and the angle if incidence.
- Solar tide
The component of the tide caused by the gravitational attraction between the Sun and water on Earth. There are two water bulges associated with this gravitational attraction. One in the direction of the sun and another on the opposite side of the Earth.
The period* of the solar tide*s is driven by the rotation of the Earth around its own axis which occurs once every 24 hours. The interaction between the solar and lunar tides cause the monthly spring/neap tidal cycle.
A solution is formed when one substance is dissolved into another. In a solution, the solute is the material present in the lesser amount. In other words it is the minor component. Contrast with solvent: the material present in a greater amount.
There are many different media into which materials are be dissolved. Commonly water is the solvent and a solute is the material dissolved in the water.
A solution is formed when one substance is dissolved into another. In a solution, the solvent is the material present in the greater amount. In other words it is the major component. Contrast with solute: the material present in a lesser amount.
There are many different media into which materials are be dissolved. Commonly water is the solvent into which solutes are dissolved.
- specular reflection
The type of reflection* that occurs off of smooth surfaces. When specular reflection* occurs, the organization of the incident light rays are preserved in the reflected ray*s. The preservation of this organization allows us to seek images reflected off of smooth surfaces such as calm water in a pool, a glass window or a mirror. Contrast with diffuse reflection* which occurs off of rough surfaces.
- Spring Tide
The tides with the largest range in the monthly cycle. Spring tide*s occur when the tidal bulges from the sun and moon are in phase. Under these conditions, the gravitational force of the sun and moon work together (interfere constructively) resulting is relatively large tidal ranges. Spring tides occur at full and new moons when the Sun and Moon are in line with each other relative to the Earth.
- Surface wave
Physical wave*s that move along the boundary between two media. The energy in these waves propagate along the surface. As the energy moves along the surface, particles of the media travel in a circular motion. The amount of particle movement (amplitude* of the wave) is greatest right at the boundary and decreases with distance from the boundary. Movement of particles penetrates into the material to a distance that is roughly 1/2 the wavelength* of the wave. Deep water ocean waves are an example of surface wave*s.
The DNA polymerase*s responsible for replication need a short priming sequence. The need for a priming sequence prevents the enzyme from starting replication at the extreme 5’ end of linear DNA. The inability to replicate the extreme 5’ linear chromosomes causes the chromosome to get a little shorter during each round of replication. The presence of the telomeric sequence means that short lengths of non-coding, repetitive sequence are lost rather than functional stretches of DNA.
- Total internal reflection
The situation in which light rays that hit a transparent surface reflect back into the original medium instead of passing through. It occurs when the angle of an incident ray of light exceeds the critical angle for two materials that meet at that surface. The critical angle is a function of the index of refraction of the two materials.
- Transverse wave
A wave* in which the displacement of the particles (or medium) is perpendicular to the direction the wave is traveling. Unlike longitudinal wave*s, these waves require solid material. They do no move through liquids or gases.
- Visible light
The range of electromagnetic radiation visible to the human eye. It is a narrow portion of the electromagnetic spectrum* encompassing energy with wavelength*s from around 400 nm (blue light) to 700 nm (red light).
The visible range of the electromagnetic spectrum is flanked by shorter wavelength ultraviolet energy on one side and the longer wavelength near-infrared energy on the other. Visible light* includes energy in the range of the sun’s peak output which is roughly 580 nm (yellow light).
The amount of three dimensional space an object occupies.
A movement or oscillation that spreads from a defined point. There are two types, physical wave*s and electromagnetic wave*s. Physical waves require a medium through which to propagate. Electromagnetic waves do not. When a wave moves, energy is propagated, not the medium through which the wave travels.
The distance over-which a wave*’s shape repeats. For transverse wave*s, the wavelength* is often drawn as a line from wave crest to wave crest, but it does not need to be. The wavelength is is the horizontal distance between successive crests, troughs or any other equivalent point between neighboring waves.
The fact that wavelength can be measured as the distance between any corresponding points on adjacent waves important for longitudinal wave*s, which lack crests and troughs. For these waves, wavelength can be shown as the distance between neighboring regions of compression.
As a distance, wavelengths are usually reported in meters with or without a prefix (kilo, micro, nano, etc).
the force created when a mass* is acted on by an external force such as gravity