DNA Structure, Replication, and Repair

Nucleotide

DNA monomer made of deoxyribose, a phosphate group, and a nitrogenous base

Deoxyribose

The pentose (five-carbon) sugar in DNA

Nitrogenous Base

The part of a nucleotide that varies (A, G, C, T)

Purine

Double-ring bases, adenine (A) and guanine (G)

Pyrimidine

Dingle-ring bases, cytosine (C) and thymine (T); uracil (U) only in RNA

Phosphodiester Bond

Covalent bond linking nucleotides into a strand's sugar-phosphate backbone

Double Helix

Two DNA strands wound around each other.

Sugar-Phosphate Backbone

The outside of each strand

Antiparallel

The two strands run in opposite directions (5' to 3' and 3' to 5')

Complementary Base Pairing

A with T, C with G, joined by hydrogen bonds; one purine with one pyrimidine

Hydrogen Bond

Weak, non-covalent bond between paired bases, easily broken

Major and Minor Grooves

Exposed edges of bases along the helix where DNA-binding proteins attach

Chargaff’s Rule

Purines equal pyrimidines; A = T and G = C

Genetic Code

The sequence of the four bases that carries the instructions to build an organism

Gene

Segment of DNA with the information for one functional molecular product

Transcription

Copying DNA into RNA, preserving base order

mRNA

Messenger RNA, carries instructions for a protein

tRNA

Transfer RNA, functional RNA needed for protein synthesis

rRNA

Ribosomal RNA, functional RNA needed for protein synthesis

Heredity

Transmission of genetic information to the next generation

Chromatin

DNA plus its packaging protein

Euchromatin

More unwound chromatin; genes available for transcription

Heterochromatin

More condensed chromatin; most genes unavailable

Supercoiled

Extremely condensed chromatin during cell division

Nucleoid

Region of a prokaryote cell holding its single circular chromosome

DNA Replication

Copying DNA before cell division

Semi-conservative Replication

Each new helix has one old and one new strand

Template

An existing strand used to build the complementary one

Origin of Replication (Ori)

Specific DNA site where replication starts

Replisome

Multi-protein molecular machine that carries out replication

Replication Bubble

Opened region at the ori

Replication Fork

Y-shaped opening where unwinding and synthesis occur

dNTP

Deoxyribonucleoside triphosphate; the nucleotide building blocks for DNA synthesis

Primer

Short RNA sequence that gives DNA polymerase a free 3' end

Leading Strand

Continuously synthesized strand

Lagging Strand

Discontinuously synthesized strand

Okazaki Fragments

Short stretches of the lagging strand

DNA Polymerase

Builds new DNA 5' to 3' and proofreads

Helicase

Unwinds the helix at the fork

Topoisomerase (DNA Gyrase)

Relieves torsional tension ahead of the fork

Single-strand Binding Proteins (SSBP)

Keep separated strands apart

Primase

Makes the RNA primer

Sliding Clamp

Holds DNA polymerase in place

DNA Ligase

Joins Okazaki fragments and seals gaps with a phosphodiester bond

Nucleases

Enzymes that degrade the leftover single-stranded overhang

Telomerase

Enzyme with a built-in RNA template that re-lengthens telomeres

Telomere

Repetitive, non-coding sequence at the tips of linear chromosomes (human TTAGGG)

Overhang

Short single-stranded stretch left on the lagging-strand template at the end

Senescence

Aging; loss of ability to make new cells to repair tissue

Proofreading

Polymerase removes a mis-paired nucleotide during replication

Mismatch Repair

Post-replication scanning and correction of mismatches

Nucleotide Extension Repair

Cuts out damaged DNA, fills it in, ligase seals

Thymine Dimer

Cross-linked adjacent thymines caused by UV light, creating a kink

Xeroderma Pigmentosum

Inherited disorder of non-functional NER with very high skin cancer risk

Mutation

Change in DNA sequence, typically one nucleotide (point mutation)

Substitution, Deletion, Insertion

The point mutation types

Germ-Line Mutation

Heritable mutation that adds to variation

Oncogenes and Tumor Suppressor Genes

Cell-cycle regulating genes whose mutation can cause cancer