Chapter 4

Purine

A class of small, nitrogen-containing, double-ringed bases (guanine, adenine) found in nucleotides.

Pyrimidine

A class of small, nitrogen-containing, single-ringed bases (cytosine, uracil, thymine) found in nucleotides.

Ribose

A five carbon sugar with an aldehyde functional group in its linear form with a chemical formula C5H10O5

Phosphate Group

A functional group or radical comprised of phosphorus attached to four oxygen, and with a net negative charge, thus represented as PO4-.

Nucleic Acid

A macromolecule composed of nucleotide monomers. Generally used by cells to store or transmit hereditary information. Includes ribonucleic acid and deoxyribonucleic acid.

Nucleotide

A molecule consisting of a five-carbon sugar, a phosphate group, and one of several nitrogen-containing bases. DNA and RNA are polymers of nucleotides containing deoxyribose and ribose respectively. Equivalent to a nucleoside plus one phosphate group.

Complementary Strand

A newly synthesized strand of RNA or DNA that has a bade sequence complementary to that of the template strand.

Adenine (A)

A nitrogenous base, one member of the base pair a-T (thymine). (biochemistry)Purine base found in DNA paired with Thymine, in RNA paired with Uracil.

Deoxyribonucleic Acid (DNA)

A nucleic acid composed of deoxyribonucleotides that carries the genetic information of a cell. Generally occurs as two intertwined strands, but these can be separated.

Ribonucleic Acid (RNA)

A nucleic acid composed of ribonucleotides that usually is single stranded. Functions include structural components of ribosomes, transporters of amino acids, and messages of the DNA code required for protein synthesis among others.

Ribonucleotide

A nucleotide found in mRNA where the sugar is ribose.

Sketch a nucleotide, label its three basic parts, and identify the 2', 3', and 5' carbons.

A nucleotide has a sugar or deoxyribose group, a phosphate that is attached on the 5' carbon and an organic nitrogenous base which is attached to the 3' carbon. Ribose has an -OH on the 2' carbon, Deoxyribose has a H' on the 2' carbon.

Deoxyribonucleotide

A nucleotide having a purine or pyrimidine base bonded to deoxyribose, which in turn is bonded to a phosphate group.

Guanine (G)

A purine base found in DNA and RNA; pairs with cytosine.

Cytosine (C)

A pyrimidine base found in DNA and RNA that pairs with guanine.

Hairpin

A secondary structure in RNA consisting of a stable loop formed by hydrogen bonding between purine and pyrimidine bases on the same strand.

X-ray Crystallography

A technique for determining the three-dimensional structure of large molecules, including proteins and nucleic acids, by analysis of the diffraction patterns produced by X-rays beamed at crystals of the molecule.

Stem-and-Loop Structure

The structure of tRNAs is so termed because it has four base paired stems and three loops (not base paired), one of which contains the anticodon.

Deoxyribose

The sugar component in the side chains of DNA.

Phosphorylation

The transferring of phosphoryl group from a donor to the recipient molecule.

Thymine (T)

Thymine is paired with Adenine in DNA sequences and is replaced by Uracil in mRNA.

Explain why RNA, and not DNA, was probably the first self-replicating molecule, and describe at least one piece of experimental evidence that supports this hypothesis.

To make a copy of itself, the first living organism had to provide a template that could be copied and catalyze polymerization reactions that would link monomers into a copy of that template. RNA is capable of both. One experimental evidence is by Wendy Johnston and David Bartel. They found that ribozymes isolated in each round are copied, the molecules that result are not identical in terms of their primary sequence because mutations were introduced during the copying step. By isolating the best enzyme and copying them in the next round, they continually selected ribozymes that were more efficient. This was to mimic the process of natural selection

Major Groove

Analysis of DNA structure, there are two types of grooves that can be seen; the major groove has the nitrogen and oxygen atoms of the base pairs pointing inward toward the helical axis. The major groove is more dependent on base composition and may be the site for protein recognition of specific DNA sequences or regions.

Ribozyme

And RNA molecule that can act as a catalyst, that is, speed up a chemical reaction.

Phosphodiester Linkage

Chemical linkage between adjacent nucleotide residues in DNA and RNA. Forms when the phosphate group of one nucleotide condenses with the hydroxyl group on the sugar of another nucleotide.

Explain why and how the secondary structure of DNA allows organisms to store and copy information.

Complementary base pairing allows each strand of a DNA molecule to be copied exactly, producing two daughter molecules. DNA's primary structure serves as a mold or template for the synthesis of a complementary strand and DNA contains the information required for a copy of itself to be made.

Nitrogenous Base

Nitrogen-bearing compound with chemical properties of a base.

Template Strand

An original nucleic acid strand used to make a new, complementary copy based on hydrogen bonding between nitrogenous bases.

Antiparallel

Describing the opposite orientation of nucleic acid strands that are hydrogen bonded to one another, with one strand running in the 5' to 3' direction and the other in the 3' to 5' direction.

Minor Groove

In the minor groove, the nitrogen and oxygen atoms point outwards.

Poly-

Many

Uracil (U)

One of the bases that is found on nucleotides of an RNA chain, which replaces Thymine from the original DNA template and therefore pairs with Adenine in RNA.

Describe the primary, secondary, tertiary, and quaternary structures of RNA, and explain in what ways RNA differs from DNA.

RNA's primary structure consists of a sequence of nitrogen-containing bases that contain information in the form of a molecular code. Its secondary structure includes short double helixes and structures called hairpins that holds RNA strands together. Its tertiary and quaternary structures that fold secondary structures into complex shapes or hold different RNA strands together. RNA has Uracil instead of Thymine, it is single stranded, its ribose has an extra -OH group, and it acts as a transcript of DNA expression. Also, DNA does not have a tertiary and quaternary structure.

Sugar

Synonymous with carbohydrate, though usually used in an informal sense to refer to small carbohydrates.

3' Carbon

The 3' carbon a hydroxyl group attached to it.

5' Carbon

The 5' carbon has a phosphate group attached to it.

Sugar-Phosphate Backbone

The DNA backbone is a polymer with an alternating sugar-phosphate sequence. The deoxyribose sugars are joined at both the 3'-hydroxyl and 5'-hydroxyl groups to phosphate groups in ester links, also known as "phosphodiester" bonds.

Complementary Base Pairing

The association between specific nitrogenous bases of nucleic acids stabilized by hydrogen bonding. Adenine pairs only with Thymine (in DNA), or Uracil (in RNA), and Guanine pairs only with Cytosine.

Polymerization

The process by which many identical or similar small molecules are covalently bonded to form a large molecule.

Double Helix

The secondary structure of DNA, consisting of two antiparallel DNA strands wound around each other.

De-

Without or remove