Chapter 10: Nucleotides and Nucleic Acids

Secondary Structure

Three-dimensional arrangement of nucleic acid strands.

Denaturation

Process of separating double-stranded DNA.

Renaturation

Re-association of separated DNA strands.

Circular DNA

DNA molecules that form a closed loop.

Eukaryotic Chromosomes

Linear DNA structures found in eukaryotic cells.

Rotational Degrees of Freedom

Flexibility in polynucleotide strand structures.

Deoxyribose-Phosphate Backbone

Structural framework of DNA composed of sugars and phosphates.

C1'-N Glycosidic Bond

Bond allowing rotation in nucleotide structure.

Base Pairing

Hydrogen bonding between complementary DNA bases.

Electrostatic Interactions

Repulsion of negatively charged phosphate groups.

Base-Pair Stacking

Hydrophobic interactions between aromatic base rings.

B-DNA

Most common DNA form in solution.

A-DNA

Shorter, fatter DNA helix, dehydrated form.

Z-DNA

Left-handed DNA helix, involved in gene regulation.

Major Groove

Wide groove in DNA, protein-binding site.

Minor Groove

Narrow groove in DNA, less accessible to proteins.

Pitch of B-DNA

34 Å per turn of the helix.

Base Pair per Turn

10 base pairs in B-DNA helix.

Hydrophobic Interactions

Interactions contributing to DNA stability.

Transcription Factors

Proteins that bind to DNA regulatory regions.

Physiological Relevance of Z-DNA

Potential role in regulating DNA expression.

H-DNA

Triplex DNA with one purine-rich strand.

Cruciform DNA

Secondary structure with four-way junction in DNA.

Palindromic regions

DNA sequences that read the same forwards and backwards.

Cytosine methylation

Addition of methyl groups to cytosine residues.

5-methylcytosine

Methylated form of cytosine in DNA.

Epigenetics

Study of heritable changes without nucleotide sequence alteration.

Intercalating agents

Molecules that insert between DNA base pairs.

Ethidium bromide

Intercalating agent used in DNA visualization.

Renaturation

Reassociation of denatured DNA strands into duplex.

Reannealing

Process of realigning complementary DNA bases.

Hybrid duplexes

DNA from different species forming stable pairs.

Sequence similarity

Degree of resemblance between different DNA sequences.

Supercoiled DNA

Circular DNA with altered helical turns.

Linking number (L)

Sum of twist (T) and writhe (W) in DNA.

Twist (T)

Number of helical turns in DNA structure.

Writhe (W)

Supercoiling of DNA in three-dimensional space.

DNA gyrase

Topoisomerase introducing negative supercoils into DNA.

Negative supercoiling

Underwinding of DNA, facilitating strand separation.

Topoisomerases

Enzymes that alter DNA supercoiling.

Human DNA length

Total length of human DNA is approximately 2 meters.

Aromatic macrocycles

Flat hydrophobic molecules that intercalate in DNA.

Actinomycin D

Antibiotic that intercalates into DNA, inhibiting transcription.

Nucleus

Cellular structure about 5 micrometers in diameter.

Compression

DNA is compressed over 100,000 times.

Nucleosomes

DNA wrapped around protein spools for packaging.

Histone Proteins

Two classes of chromatin proteins: histones and nonhistones.

Distinct Histones

Five known histones: H1, H2A, H2B, H3, H4.

Octameric Core

Histones H2A, H2B, H3, H4 form octamer structures.

Chromatin

Nucleoprotein complex of histones and nonhistone proteins.

Beads-on-a-string

Primary chromatin structure motif resembling beads on string.

30-nm Fiber

Secondary chromatin structure formed by nucleosome arrays.

Long Loops

30-nm fiber forms loops of 60,000-150,000 bp.

Miniband Unit

18 loops arranged radially in chromosome structure.

SMC Proteins

Aid chromosome organization and dynamics during mitosis.

RNA Structure

RNA is typically single-stranded with high conformational freedom.

Intrastrand Base Pairing

Complementary RNA sequences join within the same strand.

Secondary Structures of RNA

Includes stems, loops, bulges, and junctions.

Hairpin Structures

Formed by imperfect base pairing in RNA.

Tertiary Structures of RNA

Arise from coaxial stacking and pseudoknot formation.

tRNA

Contains 73-94 nucleotides with extensive intrastrand base pairing.

L-shaped tRNA

Phenylalanine tRNA adopts an 'L' shape.

Ribosomal RNA (rRNA)

Makes up about 2/3 of ribosome structure.

X-ray Crystallography

Technique revealing detailed ribosome tertiary and quaternary structures.

Quaternary Structure

Interactions between ribosomal proteins and rRNAs in ribosome.

Conserved Secondary Structures

Secondary features of rRNA are conserved across types.