BL2302 Molecular Biology: DNA Structure and DNA Sequencing

Practice vocabulary flashcards covering the components of nucleotides, DNA double-helix structures (B-DNA, A-DNA, Z-DNA), helical parameters, and Sanger chain-termination sequencing methodology.

ATP (Adenosine triphosphate)

A ribonucleotide consisting of adenine, ribose, and three phosphate groups, whose hydrolysis provides the energy to drive numerous cellular processes.

Nucleotide

A monomeric molecule consisting of a nitrogenous base, a five-carbon pentose sugar (ribose or deoxyribose), and one or more phosphate groups; acts as the fundamental building block of nucleic acids.

Nucleoside

A molecule composed of a nitrogenous base covalently linked to a pentose sugar (ribose or deoxyribose) without any attached phosphate groups (e.g., adenosine).

Purine bases

The double-ring nitrogenous bases found in nucleic acids, specifically adenine and guanine.

Pyrimidine bases

The single-ring nitrogenous bases found in nucleic acids, specifically cytosine, thymine (normally found only in DNA), and uracil (normally found only in RNA).

dATP (2'-deoxyadenosine triphosphate)

A deoxyribonucleotide building block of DNA consisting of adenine, a deoxyribose sugar lacking an oxygen atom at the $2'$ carbon position, and three phosphate groups (\text{\textalpha}, \text{\textbeta}, and \text{\textgamma}).

Deoxyribonucleotides

The four monomeric building blocks of DNA—dATP, dCTP, dGTP, and dTTP—each containing a $2'\text{-deoxyribose}$ sugar and one of the four bases (adenine, cytosine, guanine, or thymine).

Ribonucleotides

The four monomeric building blocks of RNA—ATP, CTP, GTP, and UTP—each containing a ribose sugar with a $2'\text{–OH}$ hydroxyl group and one of the four bases (adenine, cytosine, guanine, or uracil).

Base pairing

The specific hydrogen bonding interaction holding two complementary DNA strands together, linking guanine to cytosine and adenine to thymine.

Anti-parallel orientation

The arrangement of the two complementary strands in a DNA double helix running in opposing directions, such that one strand runs $5' \rightarrow 3'$ while the opposite strand runs $3' \rightarrow 5'$.

Phosphodiester bond

The covalent linkage connecting the $3'\text{–OH}$ group of one nucleotide's pentose sugar to the $5'$ phosphate group of the next; moving along a DNA strand in the $5' \rightarrow 3'$ direction, the phosphodiester bonds encountered are oriented $3' \rightarrow 5'$.

B-form DNA (B-DNA)

The predominant physiological conformation of DNA, characterized as a right-handed double helix with an overall width of $2\text{ nm}$ (20\text{ \text{\normalfont\r{A}}}), a helical repeat pitch of $3.4\text{ nm}$ (34\text{ \text{\normalfont\r{A}}}), an inter-base distance of $0.34\text{ nm}$ (3.4\text{ \text{\normalfont\r{A}}}), and distinct major and minor grooves.

Major groove

The wider and more accessible helical indentation running along the outer surface of a B-DNA double helix where specific base pairs are exposed for recognition by proteins.

Minor groove

The narrower helical groove winding along the outer surface of a B-DNA double helix on the side opposite the major groove.

A-DNA

An alternative right-handed double-helical conformation of DNA whose formation can be driven by the binding of specific proteins.

Z-DNA

An alternative left-handed double-helical conformation of DNA favored by specific base modifications and distinct salt conditions.

Maxam-Gilbert method

A DNA sequencing method developed in the mid-1970s based on chemical degradation of DNA; it is laborious and rarely used today aside from specialized applications.

Sanger method

A widely used, relatively straightforward DNA sequencing technique developed in the mid-1970s based on chain termination using modified dideoxynucleotides.

Fred Sanger

British biochemist ($1918\text{–}2013$) who was awarded the Nobel Prize in Chemistry in $1958$ for his work on the structure of proteins (especially insulin) and in $1980$ for his contribution concerning the determination of base sequences in nucleic acids.

2',3'-dideoxyribonucleotide (ddNTP)

A modified nucleotide lacking hydroxyl groups at both the $2'$ and $3'$ positions of the sugar ring; when incorporated into a nascent DNA chain, it causes irreversible chain termination because no $3'\text{–OH}$ is available to form the next phosphodiester bond.

Primer extension

The in vitro enzymatic synthesis of a new complementary DNA strand catalyzed by DNA polymerase using dNTPs, starting from a specific oligonucleotide primer annealed to a single-stranded DNA template.

Dye-labelled ddNTP sequencing

An automated variant of the Sanger method utilizing dideoxynucleotides labelled with distinct fluorescent dyes and a thermostable DNA polymerase, allowing all termination reactions to be performed together in a single reaction tube and detected by laser excitation.