Molecular Biology and Gene Expression

Germ Cells

Reproductive cells that are capable of passing on genetic information

Somatic Cells

Cells that only undergo replication

Vertical Transmission

Transmission of genetic information from parent to offspring

Horizontal Transmission

Transmission of genetic information within the same generation

Replication

The process by which DNA is copied in cells

Replication Fork

Unwound segment of the DNA where replication takes place

Leading Strand

DNA strand that is continuously formed during replication

Lagging Strand

DNA strand that is formed discontinuously during replication

Okazaki Fragments

Short sequences of DNA synthesized by DNA polymerase in the lagging strand

Cyclins

A family of proteins whose concentration increases and decreases at specific times during the cell cycle

DNA Damage

Abnormalities in DNA that arise due to errors in replication

DNA Repair

Mechanisms that correct DNA damages

DNA Replication

Must occur before a cell can produce two genetically identical daughter cells

Deoxyribonucleotide Triphosphate

Building blocks of DNA

DNA Helicase

Unwinds the double-stranded DNA during replication

DNA Primase

Initiates the synthesis of RNA primer which is essential for DNA replication

DNA Polymerase

Enzyme that synthesizes new DNA strands by adding nucleotides

Exonuclease

Removes RNA primers during replication

DNA Ligase

Seals the nick between Okazaki fragments in the lagging strand

DNA Topoisomerase

Enzyme that helps prevent supercoiling by creating temporary nicks in the DNA strand

Okazaki Fragments

Short segments of DNA synthesized on the lagging strand

Replication Bubbles

Sites where DNA replication occurs simultaneously in multiple places

Chromatin Structure

Reformation of the compact form of DNA after replication

Cyclin-CDK Complex

The combination of cyclins and cyclin-dependent kinases that regulate the cell cycle

Telomeres

Specialized nucleotide sequences at the end of chromosomes

Telomerase

Enzyme that replenishes telomere sequences during cell division

Mismatch Repair

Repair mechanism that corrects base mismatches during replication

Base Excision Repair

Mechanism that fixes single-base damage

Nucleotide Excision Repair

Mechanism that fixes larger DNA distortions, such as thymine dimers

Homologous Recombination

DNA repair mechanism that uses an undamaged strand as a template

Non-homologous End Joining

DNA repair mechanism for double-stranded breaks that does not use a template

Deamination

Removal of an amine group from a DNA base

Depurination

Removal of purines (guanine or adenine) from DNA

Alkylation of Base

Addition of alkyl groups to bases, leading to mutations

Base-Analog Incorporation

Replacement of normal bases by analogs during DNA replication

Thymine-Thymine Dimers

UV-induced bonding between adjacent thymine bases

Ionizing Radiation

Causes strand breaks in DNA

Oxidative Free Radical Formation

Generates modified purines like 8-hydroxy-deoxyguanosine (8-OH-dG)

Intrastrand Cross-Linkage

Cross-linking between bases on the same strand of DNA

Interstrand Cross-Linkage

Cross-linking between bases of opposite DNA strands

DNA and Protein Cross-Linkage

Cross-linking between DNA and proteins like histones

Nucleotide

Monomeric units of nucleic acids composed of a 5-carbon sugar, a nitrogenous base, and a phosphate group

Nucleoside

The bonded product of the nitrogenous base and five-carbon sugar (without a phosphate group)

Nucleic Acid

Large biomolecules containing genetic information and contribute to metabolic functions

DNA

The genetic material and blueprint for life, found within the nucleus of cells

RNA

A nucleic acid similar to DNA, but with only a single strand of nitrogenous bases

Adenine

The nitrogenous base that pairs with thymine in DNA

Guanine

A purine-derived nitrogenous base with NH2 substituent at carbon 2 and a carbonyl at carbon 6

Cytosine

A pyrimidine-derived nitrogenous base with NH2 at carbon 4 and a carbonyl at carbon 2

Thymine

A pyrimidine-derived nitrogenous base with a carbonyl group at carbon 2 and carbon 4, and CH3 at carbon 5

Uracil

A ribonucleotide replacing thymine in an RNA sequence

Nucleoside

A molecule containing a pentose sugar covalently bonded to a nitrogenous base via a β-N-glycosidic bond, without a phosphate group attached

β-N-glycosidic Bond

The bond between the sugar’s carbon (C1’) and the nitrogen in the base

Ribose

Sugar molecule with a hydroxyl group attached to C2

Deoxyribose

Sugar molecule with a hydrogen atom attached to C2

Nucleotide Formation

The process of forming a bond between a nitrogenous base and sugar, and adding phosphate groups to form nucleotides

Renaturation

The process when separated DNA strands can come back together

Adenylyl Cyclase

The enzyme that catalyzes the conversion of ATP to cAMP

Semiconservative Replication

The process by which DNA replicates to form daughter DNA molecules

cAMP

A secondary messenger that activates multiple cellular processes like cell signaling and gene expression

Chromosomes

DNA is stored in these tightly coiled structures

Chargaff’s Rule

The rule that states the amount of purines equals the amount of pyrimidines in DNA

G-C Bonding

Base-pairing interaction between guanine and cytosine

A-T Bonding

Base-pairing interaction between adenine and thymine in DNA

mRNA

A type of RNA that carries genetic information from DNA to the protein-synthesizing machinery

tRNA

The RNA molecule that serves as an adapter for translating mRNA into specific amino acids

rRNA

RNA molecule essential for ribosome assembly, binding, and translation of mRNA into proteins

sRNA

Small RNA involved in rRNA and mRNA processing and gene regulation

Nucleases

Enzymes that degrade nucleic acids, vital in nucleic acid metabolism

Ribonuclease

The enzyme that hydrolyzes RNA

Deoxyribonuclease

The enzyme that hydrolyzes DNA

Restriction Endonucleases

Enzyme that cleaves both strands of DNA at specific base sequences

CRISPR-Cas

The family of enzymes used for genome editing, involving RNA-guided cleavage

Topoisomerases

A group of enzymes that catalyze changes in DNA’s topological state by adding or removing supercoils

Helical Structure of DNA

The structure of DNA when the two strands wind around a central axis in a double helix

Template Strand

The DNA strand that contains the genetic information and is transcribed into RNA

Coding Strand

The complementary strand of DNA that matches the RNA transcript sequence

Phosphodiester Bond

The chemical bond connecting nucleotides in DNA and RNA

Base-Stacking Interaction

The chemical property of bases in DNA that allows them to form base-stacking interactions

Phosphodiesterase

The enzyme involved in the hydrolysis of phosphodiester bonds between nucleotides

Recombinant DNA Technology

In vivo application technique to yield a clone of a desired DNA fragment involving isolation, recombination, and manipulation

Restriction Endonuclease (Restriction Enzyme)

An enzyme used in recombinant DNA technology to cleave DNA chains at specific locations

Chimeric Molecules

Molecules with both human and bacterial DNA sequences

CRISPR-Cas9

Clustered regularly interspersed short palindromic repeats-associated gene 9

Cas9

CRISPR-associated gene 9

Cloning

Production of large quantities of identical DNA molecules

cDNA Library

Collection of DNAs representing the genes expressed (exons) in cell or tissue type

Genomic Library

Collection of all fragments representing all DNA in the chromosome of a cell, including exons, introns, and regulatory sequences

Cloning Vector

DNA molecule into which foreign DNA can be inserted or integrated; capable of replication in the host cell

Plasmids

Circular double-stranded DNAs found in bacteria that replicate autonomously from host genome

Bacteriophage (Phages)

Virus-based vectors capable of lysogeny by infecting and reproducing in a bacterium

Cosmid

Plasmids that are a combination of bacteriophages and plasmids

BAC, YAC, and PAC

Bacterial Artificial Chromosome, Yeast Artificial Chromosome, and Artificial Chromosome on E. coli bacteriophage P1-based vectors

Probe

Pieces of DNA or RNA with phosphorus-32-containing nucleotides used to probe or search libraries for target genes

Blotting/Blot Transfer

Technique to visualize specific DNA or RNA fragments

DNA Sequencing

Method used to determine the precise order of nucleotides within a DNA molecule

Sanger Sequencing

DNA sequencing method that differentiates bases using colors (automated) or radioisotopes (manual)

Polymerase Chain Reaction (PCR)

Method to amplify a target DNA sequence with steps of denaturation, annealing, and extension/polymerization

Reverse Transcription PCR (RT-PCR)

Conversion of RNA to single-stranded DNA with amplification of the target DNA sequence

Single Nucleotide Polymorphism (SNP)

Substitution of a single nucleotide at a specific position in the genome