bio lab 3

Pyrimidine

- A nitrogen-containing, single ring compound that occurs in nucleic acids. In DNA, the pyrimidines are cytosine and thymine.

Guanine

- A nitrogenous base; pairs with cytosine in DNA molecules.

Phosphate

- A salt of phosphoric acid. A functional group that gives a negative charge to a molecule (a phosphorous atom covalently bound to four oxygen molecules, two of which are anions).

Ion

- An atom with an unequal number of protons and electrons resulting in a charge. When writing out the chemical symbol, charge is indicated with superscripts such that an atom with one more proton than electrons would have a plus sign, an atom with two more protons than electrons would have the numeral "2" followed by the plus sign (example: Mg2+) and an atom with one less proton than electrons would have a minus sign (example: Cl- ).

Hydrogen bond

- An attraction between two atoms that have opposite partial charges. These partial charges are the result of polar covalent bonds where one atom in the bond keeps the pair of shared electrons more than 50% of the time resulting in the electron-hog having a partial negative charge and the wimpy atom having a partial positive charge. While these charges are not as strong as in ions, they are still strong enough to hold atoms together.

Lysis

- Literally the word means the process of cutting/breaking. You will hear this term used to describe breaking a variety of structures from bonds to organelles. In lab today it will apply to both the process of rupturing a cell to release its constituents and to the process of denaturing DNA during PCR. In this exercise, human check (epithelial) cells are lysed to release genomic DNA for PCR

Chelex beads

- Microscopic beads that bind divalent cations (ions with two more protons than electrons) in solution. A proprietary name for a chelating agent.

Covalent bond

: A bond that is the result of two atoms sharing a pair of electrons. These electrons float around the nuclei of both atoms. Only atoms with partially filled valence shells can form covalent bonds. The pair of electrons that then act to fill empty spots in the valence shell of each atom. Covalent bonds come in two flavors: nonpolar covalent bonds -where the two atoms are equally electronegative and thus share the electrons equally, and polar covalent bonds -where one atom is much more electronegative than the other and therefore hogs the electrons so that they spend more time around its nucleus than around the nucleus of the other atom in the bond. Polar covalent bonds result in partial charges in the two atoms. The more electronegative atom becomes partially negatively charged (indicated with the symbol δ-) because, more often than not, it has more electrons than protons. The less electronegative atom becomes partially positively charged (indicated with the symbol δ+) because, more often than not, it has more protons than electrons.

Thymine -

A base found in DNA (but not in RNA) and derived from pyrimidine; pairs with adenine in DNA.

Macromolecule

A big molecule. What constitutes (counts as) big varies but, for this class, we generally mean lipids and the organic polymers: proteins, carbohydrates, and nucleic acids.

DNases

A category of nucleases, digestive enzymes that degrade nucleic acids. In the case of DNases, they break bonds between nucleotides in the phosphate-sugar "backbone" of DNA. These are often components in gene therapies for diseases like cystic fibrosis.

Pentagon

A five-sided figure.

Ethidium bromide

A fluorescent dye molecule that intercalates (inserts between) DNA base pairs and fluoresces when exposed to ultraviolet light.

Purine

A nitrogen containing, double ring compound that occurs in nucleic acids. In DNA, the purines are adenine and guanine.

Nitrogenous base

A nitrogen-containing ring molecule that, in combination with a pentose sugar and a phosphate group, form a nucleotide, the fundamental unit of nucleic acids. (See nucleotide.)

Cytosine

A nitrogenous base pairs with guanine in DNA molecules

Deoxyribonucleic acid (DNA)

A nucleic acid, normally a double-stranded helix where each strand is made of a string of nucleotide monomers, each consisting of a deoxyribose sugar, a phosphate functional group and the nitrogenous bases adenine, cytosine, guanine or thymine. DNA can be replicated and determines the inherited structure of a cell's proteins

Double helix

A pair of parallel ribbon-like helices intertwined about a common axis; a twisted ladder. This is the structure of DNA.

Deoxyribose

A pentose sugar that is a part/component of the nucleic acid DNA

Adenine

A purine nitrogenous base found in DNA and RNA; it pairs with thymine in DNA and is the complementary base to uracil in RNA.

Primer -

A short sequence of nucleotides (usually 16-24 bases in length, aka oligonucleotide) that recognizes a particular sequence of nucleotides on the target DNA sequence. Primers for the PCR are usually synthesized in a laboratory

Oligonucleotide

A short single-strand sequence of nucleotides.

Monomer

A simple compound whose molecules can join together to form polymers

Hexagon

A six-sided figure.

Enzyme

A type of molecule (generally protein) that facilitates a chemical reaction (makes it easier for the reaction to happen).

Null

A word element derived from Latin meaning "none".

Ion

An atom with an unequal number of protons and electrons. The imbalance happens when an atom interacts with another atom that has very different electronegativity. The more electronegative atom strips an electron away from the less electronegative atom. Ions with more protons than electrons are positively charged and called cations while ions with more electrons than protons are negatively charged and called anions.

Anion

An atom with more electrons than protons.

Ionic bond

An attraction between an anion and a cation. While technically stronger than a covalent bond, the presence of water in biological systems makes ionic bonds highly unstable and easy to break. Ions joined together this way are called salts or compounds

Covalent bond

An attraction between two atoms resulting from the atoms sharing a pair of electrons. Considered to be a strong bond in biological systems. Atoms joined by covalent bonds are called molecules.

Cation

An ion with more protons than electrons

dNTPs

Commonly used abbreviation for the deoxynucleoside triphosphates used in synthesizing DNA. There are four types: dATP, dTTP, dGTP, dCTP. When joined to a growing polynucleotide strand, the dNTPs lose two of their three phosphate functional groups becoming the nucleotide building blocks you see in a nucleic acid. A similar process occurs during the production of RNA (translation) as NTPs are joined (note that there is no "r" prefix for the RNA NTPs).

lipids

Energy-rich organic compounds, such as fats, oils, and waxes, that are made of carbon, hydrogen, and oxygen.

EDTA

Ethylenediamine tetraacetic acid, a common chelating agent (see chelate) often used to make iron soluble but also used for other metals.

Amplification

In PCR it is the production of a large number of copies of a specific region of DNA.

Eukaryotes

Organisms that are made of cells containing a membrane-bound nucleus that surrounds the genetic material (DNA).

Replicate

Reproduce or make an exact copy (verb) or the resulting copy (noun).

Electronegativity

The ability of an atom to attract negatively charged electrons. This is a function of the number of positively charged protons in the nucleus as well as how many electron/energy levels (or shells) the atom has. The more protons, the stronger the pull is; the more electron levels, the further away from the protons the valence shell (outermost shell) is and thus the weaker the pull is.

Complementary base pair

The chemical attraction between specific base pairs in a nucleic acid molecule. Adenine always pairs with thymine by two hydrogen bonds and guanine with cytosine by three hydrogen bonds. When DNA and RNA are joined together, the uracil of RNA pairs with adenine. Complementary base pairing is responsible for holding DNA in the form of a double helix, each base pair forming a rung of the ladder. This obligate pairing is what ensures that genetic material is replicated accurately from generation to generation.

Aliquot

The division of a quantity of material into smaller, equal parts. The term is more often used to refer to a small quantity taken from a larger amount of something

Nucleotides -

The fundamental unit of DNA or RNA; they consist of a sugar (deoxyribose or ribose), phosphate group, and nitrogenous base (adenine, thymine, cytosine, or guanine, with uracil in place of thymine in RNA).

Denature

The loss of secondary, tertiary and, in proteins, quarternary structure in nucleic acids and proteins with the application of some form of stress. In lab the forms of stress will generally either be changes in pH or temperature. In lab today, PCR will denature DNA by separating the two complementary strands. In vivo denaturation is accomplished by enzymes; in PCR, denaturation is accomplished by heat.

Valence shell

The outermost shell where electrons can be found orbiting an atom's nucleus. There is a strong pull to fill this shell so that it holds the maximum number of electrons. This results in atoms interacting, sharing, giving up, and taking electrons and forming chemical bonds as a result.

PCR pellets™

The primary ingredient for the PCR we run in class, which contains all of the necessary components (dNTPs, primer, buffer, salts, polymerase, magnesium) for PCR except for the template DNA.

Extension

The process of Taq polymerase adding dNTPs (deoxynucleotide triphosphates -- dATP, dTTP, dCTP, or dGTP) onto the ends of the oligonucleotide primers (short nucleic acids -less than 50 nucleotides long that bind to the template strand of DNA and start the process of building the complementary strand). Extension follows the basepairing rule and proceeds in the 5' to 3' direction.

PCR/Polymerase chain reaction

The process of amplifying/synthesizing DNA (making more of it) outside of a cell (in vitro).

Template

The single strand of DNA that contains the target sequence that will be copied into a complementary strand to reform a full double-stranded DNA molecule.

Atom

The smallest unit of matter that still has all of the properties of an element. Atoms consist of three sub-atomic particles: protons with a positive charge and neutrons with no charge are found together in the nucleus of the atom (not to be confused with the nucleus of a cell) and they are surrounded by a cloud of negatively charged electrons. The number of protons and electrons are the same unless the atom interacts with another one.

Molecular biology

The study of genes and the molecular details that regulate the flow of genetic information from DNA to RNA to protein, and from generation to generation.

Taq DNA polymerase

Thermostable DNA polymerase that was isolated from the thermophilic bacterium Thermus aquaticus. This DNA polymerase is commonly used in PCR.

Annealing (in PCR)

To anneal. Similar to the use of the term in metallurgy, it refers to using exposure to high temperatures alternating with exposure to cooler temperatures to change the chemical properties of a substance. In biology, and in particular in PCR, this is used to refer to the bonding of the primers to template strands of DNA. High temperatures are used to split the double-stranded DNA molecule and then the temperature is lowered so that the primers can bind to each single strand of DNA. The term anneal is often used to refer only to the binding of primers to the target DNA sequence.

Chelate

To bind metal ions to complex ligands, which deactivates the metal ion and makes it soluble (can dissolve in solution). The resulting complex prevents the metal from engaging in chemical reactions as it would in isolation. An example of a common chelating agent is ethylenediamine tetraacetic acid, EDTA, see below. Chelation therapy is the standard treatment for toxic metal poisoning. It has also been promoted by some as a treatment for a variety of other diseases although current research does not support this.

Molecule

Two or more atoms joined together by covalent bonds. -A molecule may also have ionic and hydrogen bonds but the presence of covalent bonds is the defining requirement for a molecule.

nucliec acid

a complex organic substance present in living cells, especially DNA or RNA, whose molecules consist of many nucleotides linked in a long chain.

Proteins

amino acids, Nutrients the body uses to build and maintain its cells and tissues

Polymer

molecules composed of many monomers; makes up macromolecules

Carbohydrates

the starches and sugars present in foods, break down to glucose for energy