Biochem

Purines

Adenine and guanine; nitrogenous bases containing two fused rings.

Pyrimidines

Cytosine thymine and uracil; nitrogenous bases containing one ring.

Adenine (A)

A purine found in both DNA and RNA.

Guanine (G)

A purine found in both DNA and RNA.

Cytosine (C)

A pyrimidine found in both DNA and RNA.

Thymine (T)

A pyrimidine found in DNA but not RNA.

Uracil (U)

A pyrimidine found in RNA instead of thymine.

Nucleoside

A nitrogenous base attached to a sugar.

Nucleotide

A nitrogenous base attached to a sugar and one or more phosphate groups.

Nucleotide substrates

The nucleotide molecules used by DNA and RNA polymerases to synthesize nucleic acids.

AMP

Adenosine monophosphate.

ADP

Adenosine diphosphate.

ATP

Adenosine triphosphate.

GMP

Guanosine monophosphate.

GDP

Guanosine diphosphate.

GTP

Guanosine triphosphate.

CTP

Cytidine triphosphate.

UTP

Uridine triphosphate.

Ribose

The five-carbon sugar found in RNA; contains a hydroxyl group at the 2' carbon.

2'-Deoxyribose

The five-carbon sugar found in DNA; contains hydrogen instead of a hydroxyl group at the 2' carbon.

1' Carbon

The sugar carbon attached to the nitrogenous base.

2' Carbon

The sugar carbon that distinguishes ribose from 2'-deoxyribose.

3' Carbon

The sugar carbon containing the hydroxyl group involved in nucleic acid polymerization.

4' Carbon

A numbered carbon that forms part of the five-carbon nucleotide sugar.

5' Carbon

The sugar carbon attached to the phosphate group.

2'-Deoxy Prefix

Indicates that the 2' carbon contains hydrogen instead of hydroxyl.

DNA Double Helix

A double-stranded helical structure consisting of two complementary antiparallel strands.

Antiparallel DNA

Two DNA strands running in opposite directions; one 5' to 3' and the other 3' to 5'.

DNA Directionality

The direction of a DNA strand is determined by its sugar-phosphate backbone and numbered sugar carbons.

Sugar-Phosphate Backbone

The repeating sugar and phosphate structure forming the outside of nucleic acids.

DNA Base Location

Nitrogenous bases are positioned inside the double helix while the sugar-phosphate backbone is on the outside.

A-T Base Pairing

Adenine and thymine pair through two hydrogen bonds.

G-C Base Pairing

Guanine and cytosine pair through three hydrogen bonds.

A-U Base Pairing

Adenine and uracil pair through two hydrogen bonds in RNA.

Hydrogen Bond Donor

A chemical group that provides a hydrogen for hydrogen bonding.

Hydrogen Bond Acceptor

An atom or chemical group that accepts a hydrogen bond.

DNA Base-Pair Geometry

Canonical DNA base pairs have similar overall geometry despite having different hydrogen-bonding patterns.

B-DNA

The most common hydrated form of DNA; a right-handed double helix with approximately 10.4 base pairs per turn.

A-DNA

A more compact right-handed nucleic acid conformation favored under dehydrated conditions.

Z-DNA

A distinctive left-handed DNA helix with a zigzag-shaped backbone.

B-DNA Dimensions

Approximately 3.4 angstroms between base pairs; 34 angstroms per turn; 20 angstroms in width.

B-DNA Hydration

B-DNA is the most common hydrated DNA conformation.

A-DNA Formation

Dehydration causes B-DNA to transition into the more compact A-form structure.

Double-Stranded RNA

Typically adopts an A-form helical structure.

DNA and RNA Sugar Difference

DNA contains 2'-deoxyribose while RNA contains ribose with a 2'-OH group.

DNA Nitrogenous Bases

Adenine guanine cytosine and thymine.

RNA Nitrogenous Bases

Adenine guanine cytosine and uracil.

Major Groove

The wider and more accessible groove of DNA where most DNA-binding proteins interact.

Minor Groove

The narrower and less accessible groove of DNA.

DNA-Binding Proteins

Proteins that recognize specific DNA sequences through interactions with chemical groups exposed along the DNA grooves.

Major Groove Recognition

Proteins identify DNA sequences by recognizing patterns of hydrogen-bond donors and acceptors along base-pair edges.

DNA Protein Interactions

Proteins interact with DNA through hydrogen bonding and other molecular interactions within the grooves.

Complementary DNA Strands

Two DNA strands whose nucleotide sequences are determined by complementary base-pairing rules.

DNA Sequence Direction

DNA sequences are conventionally written in the 5' to 3' direction.

DNA Complementary Base Rules

A pairs with T and G pairs with C.

Antiparallel Base Pairing

Complementary DNA strands must run in opposite directions.

Palindromic DNA Sequence

A DNA sequence with symmetry when both complementary strands are read in the 5' to 3' direction.

Dyad Symmetry

The symmetrical arrangement associated with palindromic DNA sequences.

Palindromic Sequence Recognition

Specific regulatory proteins recognize palindromic DNA sequences through their symmetrical molecular patterns.

Circular DNA

DNA whose ends are covalently connected to form a continuous circular molecule.

Phosphodiester Linkage

A covalent bond connecting the 3'-OH of one nucleotide to the 5' phosphate of another nucleotide.

Circular DNA Formation

A bridging phosphate connects the 3' and 5' ends of the DNA backbone.

DNA Topology

The structural arrangement and linking of DNA strands within a molecule.

Topologically Linked DNA

DNA strands that are interlinked and must be separated through appropriate enzymatic processes.

DNA Strand Separation

The process of separating complementary DNA strands so they can be replicated or read.

DNA Supercoiling

Additional twisting of DNA beyond its normal double-helical structure.

Overwound DNA

DNA that has been twisted more tightly than its normal helical structure.

Supercoiled DNA Example

The lecture describes overwound DNA containing approximately 12 base pairs per turn compared with approximately 10 to 10.4 in B-DNA.

DNA Compaction

Supercoiling helps compact long DNA molecules so they can fit inside cells and nuclei.

DNA Genome Size

DNA molecules vary greatly in size from viral genomes containing thousands of base pairs to human genomes containing billions.

RNA Hairpin

A structure formed when complementary regions of one RNA strand base-pair with each other.

Stem-Loop Structure

Another name for an RNA hairpin structure.

RNA Hairpin Stem

The region of a hairpin where complementary bases form hydrogen bonds.

RNA Hairpin Loop

The unpaired region connecting the two sides of a hairpin stem.

Intramolecular Base Pairing

Base pairing between complementary regions of the same nucleic acid strand.

RNA Tetraloop

A loop containing four nucleotides.

UUCG Loop

A common stable four-nucleotide RNA loop that forms favorable internal interactions.

RNA Primary Structure

The linear sequence of nucleotides.

RNA Secondary Structure

Local RNA folding arrangements such as stems and hairpins formed through base pairing.

RNA Tertiary Structure

The overall three-dimensional folding of RNA involving interactions between distant regions of the molecule.

RNA Folding

RNA folds through base pairing and additional molecular interactions to form complex secondary and tertiary structures.

Noncanonical Base Pairing

Base pairing that does not follow standard Watson-Crick pairing rules.

G-U Wobble Pairing

A noncanonical base pair between guanine and uracil that occurs commonly in RNA.

G-U Pair Stability

G-U wobble pairs are generally less stable than G-C pairs.

RNA Tertiary Interactions

Interactions between stems loops bases and the sugar-phosphate backbone that contribute to three-dimensional RNA structure.

Ribozyme

An RNA molecule that functions as an enzyme and catalyzes chemical reactions.

Ribozyme Discovery

The catalytic activity of RNA was discovered in the 1980s.

Ribozyme Active Site

A region formed by RNA folding where catalytic activity occurs.

Self-Splicing RNA

RNA that catalyzes its own splicing.

RNA Catalytic Function

Some RNA molecules can catalyze reactions instead of functioning only as genetic messengers.

DNA Replication

The process of producing new DNA molecules from an existing DNA molecule.

Transcription

The process of synthesizing RNA using DNA as a template.

Translation

The process of using RNA information to synthesize proteins.

Central Dogma

The flow of genetic information from DNA to RNA to protein.

DNA Polymerase

The enzyme responsible for synthesizing new DNA strands.

RNA Polymerase

The enzyme responsible for synthesizing RNA from a DNA template.

Messenger RNA (mRNA)

A single-stranded RNA copy of the genetic information from a particular DNA gene.

Gene Expression

The process through which genetic information encoded in DNA is used to produce functional RNA or proteins.

DNA Genetic Stability

Double-stranded DNA serves as the stable inherited genetic material in most organisms.

Meselson-Stahl Experiment

A classic experiment demonstrating that DNA replication is semiconservative.