107: Index

I-1

A. See Adenine; Alanine

A site, of ribosomes

AAA⁺ protein

Abasic site

Abortive initiation, of bacterial transcription

Abrin, translation inhibition by

Absolute temperature (T)

Accommodation, in elongation

Acetylation, of amino acids

histone tails and

N⁴-Acetylcytidine

Acetyllysine

Achiral molecule

Acid dissociation constant (K_a)

Acidic solution, pH of

Acinetobacter baylyi

AcMNPV. See Autographa californica multicapsid nucleopolyhedrovirus

Acquired immune deficiency syndrome (AIDS)

retrovirus and

reverse transcriptase inhibitors for

Acridine

Actin

Actinomycin D

Activation

Activation energy

catalysts and

enzymes and

transition state and

Activators

DNA looping and

in feedback loops

groups of genes regulated by

nucleosomes and

for positive regulation of eukaryotic promoters

RNA polymerase control by

separate DNA-binding and regulatory domains of

in signal integration

structural motifs of

transcription. See Transcription activators

Active sites, on enzymes

Adaptation, of living systems

Adaptor hypothesis

ADAR. See Adenosine deaminase acting on RNA

Adenine (A)

alkylation of

base pairing with

deamination of

DMS and

in DNA structure

early studies of

hydrogen bonding with

melting temperature and

methylation of

modification of

nomenclature for

oxidative damage to

in prebiotic chemistry

in RNA structure

pairing of

substitution of

structure of

synthesis of

Adenosine

in cofactors

nomenclature for

RNA editing of

structure of

Adenosine 2′-monophosphate

Adenosine 3′,5′-cyclic monophosphate (cAMP)

in gene expression regulation

lac operon and

Adenosine 3′-monophosphate

Adenosine 5′-monophosphate

Adenosine deaminase acting on RNA (ADAR)

Adenosine diphosphate (ADP)

energy storage and release with

nomenclature for

Adenosine monophosphate (AMP)

nomenclature for

types of

Adenosine triphosphate (ATP)

DNA helicases and

DNA ligase and

energy storage and release with

evolution of

hydrolysis of

Michaelis-Menten kinetics for

for motor proteins

nomenclature for

nucleoside diphosphate kinase binding to

in pyrosequencing

RecA and

T4 RNA ligase with

S-Adenosylmethionine (adoMet)

adenosine role in

in mRNA capping

Adenylate

nomenclature for

structure of

Adenylyl cyclase

Adenylylation

Adenylylation step, of aminoacyl-tRNA synthetases

A-DNA. See A-form DNA

AdoMet. See S-Adenosylmethionine

ADP. See Adenosine diphosphate

ADP-ribosylation

histone tails and

Adriamycin. See Doxorubicin

Adult stem cells

Aequorea victoria

Aequorin

Affinity chromatography

for protein purification

terminal tags for

A-form DNA (A-DNA)

A-form RNA (A-RNA)

Africa, human evolution in

African sleeping sickness

Age-related disease, telomeres and

Agrawal, Rajendra

Ahringer, Julie

AIDS. See Acquired immune deficiency syndrome

Ala. See Alanine

Alanine (Ala, A)

chemical properties of

enantiomers of

in protein folding

Ramachandran plot for

in secondary structures

structure of

Alberts, Bruce

Alcohol dehydrogenase, reaction rate of

Alhazen

Alkaline phosphatase

Alkaptonuria

Alkylation, DNA alterations by

Alleles

codominance of

incomplete dominance of

independent assortment of

linked genes

nonindependent segregation

unlinking of

replacement of, with site-specific recombination systems

segregation of

Allis, C. David

Allolactose

Allopatric speciation

Allosteric effector, in protein folding

Allosteric enzymes

binding sites of

kinetic properties of

modulators of

Allosteric modulators

Allosteric proteins. See Allosteric enzymes

Alpha carbon atom (C_α)

of amino acids

I-2

as chiral center

in initial model

in NMR

in polypeptide chains

thick-line trace of

Alpha helix

in DNA-binding

frequency of

in prion-based misfolding diseases

structure of

in supersecondary structures

with β sheet

Alpha/beta barrel

Alternative RNA splicing

in Drosophila melanogaster

sex determination and

stress and

Alu transposon

Alzheimer disease

linkage analysis for

mutations and

α-Amanitin

Ambros, Victor

Amelogenin gene

Ames, Bruce

Ames test

Amine group, uncharged

Amino acids

abbreviations for

in α helix

in β conformation

biosynthesis of, transcription and

as chemical building blocks

chemical modification of

chemical properties of

chirality of

codons of

common

ionic bonds between

oligonucleotide-directed mutagenesis

polypeptide chains of

in protein folding

protein function and

in protein synthesis

activation of

attachment to tRNA by aminoacyl-tRNA synthetases

initiation with

proofreading of

unnatural

R groups of

nonpolar, aliphatic

nonpolar, aromatic

polar, charged

polar, uncharged

site-directed mutagenesis

structure of

substitutions of

tRNA and

α-Amino acids

Amino group

Amino terminus

Aminoacyl-tRNA

ribosome binding by

Aminoacyl-tRNA synthetases

amino acid activation by

amino acid attachment to tRNA by

evolution of

fidelity and proofreading of

Aminoglycosides, translation inhibition by

AMP. See Adenosine monophosphate

Amphenicols, translation inhibition by

Amphipathic helix

Ampicillin, resistance to

Analytes

Anaphase

in meiosis

in mitosis

Aneuploidy

Anfinsen, Christian

Annealing

cross-species

in oligonucleotide-directed mutagenesis

Antagomirs

Anthracyclines

Antiaging therapy

Antibiotics

quinolone. See Quinolone antibiotics resistant to

plasmids with

transmittance of

transposons

translation inhibition by

Antibodies

disulfide bonds in

van der Waals interaction in

in Western blotting

Anticodons

mutation suppression and

wobble and

Antigens, van der Waals interaction in

Antimutator DNA polymerase

Antiparallel β sheet

in supersecondary structures

Antiparallel double helix

Antitermination mechanism

AP-1 transcription activators

AP endonuclease

APOBECs

Apoenzyme

Apoprotein

Aqueous solutions

Arabidopsis thaliana

basic information on

DNA of

as model organism

telomere sequence of

Arabinose

AraC protein

Arago, Dominique

Arber, Werner

Archaea

evolution of

genome databases of

Architectural regulators

AREs. See AU-rich elements

Arginine (Arg, R)

ADP-ribosylation of

chemical properties of

DNA-binding of

in histone

ionic bonds between

methylation of

histone tails and

in protein folding

in secondary structures

structure of

Arginine auxotrophs

Argonaute

Aristotle

A-RNA. See A-form RNA

Arnheim, Norman

ARS. See Autonomously replicating sequences

Artemis

Artificial chromosomes

bacterial. See Bacterial artificial chromosomes

human. See Human artificial chromosomes

yeast. See Yeast artificial chromosomes

Ashe, Mark

Asian flu pandemic

Asn. See Asparagine

Asp. See Aspartate

Asparagine (Asn, N)

chemical properties of

DNA-binding of

glycosylation of

in protein folding

in secondary structures

structure of

Aspartate (Asp, D)

chemical properties of

in protein folding

in secondary structures

structure of

Association constant (K_a), in protein-ligand interaction

Astbury, William

Asymmetric cell divisions

Atomic orbitals

ATP. See Adenosine triphosphate

ATPases

ATP-binding proteins

sequence and

structure of

ATP-coupling stoichiometry

Attenuation

transcription

translation

AU-rich elements (AREs)

Aurodox, translation inhibition by

Australopithecus

Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV)

Autoinducer synthase enzymes

Autoinducers

Autoinhibition, of protein function

Autonomously replicating sequences (ARS)

Autoradiograph

I-3

Autosomes

Auxotrophs

Avery, Oswald T.

Avian influenza

Avidin

dissociation constant for

in indirect immunofluorescence

Avilamycin, translation inhibition by

3′-Azido-3′-deoxythymidine (AZT)

development of

for HIV infection

reversible inhibition by

Azithromycin, translation inhibition by

AZT. See 3′-Azido-3′-deoxythymidine

B lymphocytes

Bacmids

Bacon, Francis

Bacon, Roger

BACs. See Bacterial artificial chromosomes

Bacteria. See also Escherichia coli

BER in

biological information flow in

chromosomes in

forms of

maintenance of

size of

DNA replication in

elongation factors of

evolution of

functions of

gene regulation in. See Gene regulation in bacteria

genome sequencing of

horizontal gene transfer in

initiation factors of

mRNA and ribosomal subunit attachment in

NER in

origin of replication in

plasmids in

promoters of

radiation resistance of

recombinant proteins from

replication fork in

ribosomes in

RNA degradation in

signal sequences of

SMC proteins in

tmRNA rescue in

transcription in. See Transcription

transposition of

Bacterial artificial chromosomes (BACs)

in Human Genome Project

Bacterial DNA, organization of

Bacterial flagella

Bacterial plasmids. See Plasmids

Bacterial RecA recombinase. See RecA protein

Bacterial ribosome, crystallization of

Bacterial transcription factors, structure of

Bacterial transduction

Bacterial transposons

Bacteriophage Mub

Bacteriophage N4 virion RNA polymerase

Bacteriophage P1

DNA circularization

site-specific recombination

Bacteriophage T4

DNA and viral particles of

group I introns in

RNA ligase

Bacteriophage T7

DNA and viral particles of

DNA polymerase of

for recombinant proteins

RNA polymerase of

Bacteriophage λ

DNA and viral particles of

gene regulation in

growth and life cycle of

infection with

map of

site-specific recombination in

λ repressor in

Bacteriophage λ exonuclease

Baculoviruses, recombinant proteins from

Baltimore, David

BamHI

Bardet-Biedl syndrome (BBS)

Barnett, Leslie

Barr body

Bartel, David

Base excision repair (BER)

replisome at

Base pairs

of codon and anticodon

in DNA polymerase I

in DNA replication

formation of

in mRNA and ribosomal subunit attachment

mutations of

indel

point mutation

for nanotechnology

in RNA

with snRNAs

triples

wobble

Base stacking

in RNA

Bases. See also Purines; Pyrimidines

methylation of

in DNA

in RNA

nomenclature for

in RNA editing

structure of

Basic helix-loop-helix motif, in transcription factors

Basic leucine zipper motif, in transcription factors

Basic Local Alignment Search Tool (BLAST) algorithm

Basic solution, pH of

Bassler, Bonnie

Bateson, William

BBS. See Bardet-Biedl syndrome

BBS5 gene

B-DNA. See B-form DNA

Beadle, George

Belfort, Marlene

Bending, in DNA structure

Benner, Steve

Bentonite, prebiotic evolution role of

Benzaldehyde, reaction rate of

Benzer, Seymour

Benzo[a]pyrene

Benzyl alcohol, reaction rate of

BER. See Base excision repair

Berg, Paul

Berger, James

Beta barrel

GFP

Beta clamp protein, DNA binding to

Beta conformation

frequency of

structure of

Beta hairpin

Beta sheet

in prion-based misfolding diseases

in quaternary structure

in ribbon diagrams

structure of

in supersecondary structures

with α helix

Beta sliding clamps

discovery of

DNA ligase and

Okazaki fragments and

Pol I and

of Pol III holoenzymes

chromosomal replicase and

trombone model and

Beta subunit, of DNA polymerase

Beta turns

Beta-alpha-beta motif

in zinc finger domain

B-form DNA (B-DNA)

relaxed

supercoiling of

underwinding of

B-form RNA (B-RNA)

Bicoid activator

Bidirectional DNA replication

Biggin, Mark

Binding, reversible

in protein-ligand interactions

quantification of

Binding energy (ΔG_B)

Binding motifs

Binding site, in protein-ligand interactions

Biochemical standard free-energy change (ΔG′°)

Biocytin

Biological information

chemical basis of

classification of

DNA for

flow of. See Information flow

life requirement of

minimum requirements of

I-4

pathways of

transfer of. See DNA replication

Biotechnology

affinity chromatography in

birth of

cloning. See DNA cloning

enzymes for

gel electrophoresis. See Gel electrophoresis

genome editing with recombination

homing endonucleases in

hybridization techniques

methods of

Northern blotting

polymerase chain reaction

recombinant DNA. See Recombinant DNA

recombinant proteins. See Recombinant proteins

RNAi

site-specific recombinases

site-specific recombination in

Southern blotting

transposons

Biotin

dissociation constant for

in indirect immunofluorescence

Bird influenza

Blackburn, Elizabeth

BLAST algorithm. See Basic Local Alignment Search Tool algorithm

Bleomycin

Blobel, Günter

Block, Stephen

Blood, pH of

Blood type

Blunt ends

Bmp4

Bond angle

of peptide bonds

Bonds, chemical

electrons in

energy transfer in

molecular behavior and

quantum mechanical terms of

weak. See Weak chemical interactions

Bonobos

evolution of

humans and

Boveri, Theodor

Bovine spongiform encephalopathy (BSE)

Boyer, Herbert

Brainbow method

Branch migration

with RecA protein

Branch point

Branching evolution

BRCA1 gene

BRCA1 protein

BRCA2 gene

BRCA2 protein

Bread mold. See Neurospora crassa

Breaker, Ronald

Brenner, Sydney

Brevig Mission strain

Bridges, Calvin

Briggs, G. E.

B-RNA. See B-form RNA

Brock, Thomas

Bromodomains

Brown, Patrick O.

Brown, Robert

Brownell, Jim

Bryant, Zev

BSE. See Bovine spongiform encephalopathy

Budding yeast. See Saccharomyces cerevisiae

Buffer solution

in column chromatography

Buffering capacity

Building blocks, chemical

of nucleic acids

postsynthetic changes

of proteins

structure with

Burley, Stephen

Bustamante, Carlos

Butterfly

Byrne, Rose

C. See Cysteine; Cytosine

Caenorhabditis elegans

basic information on

DNA of

as model organism

RNAi in

transposons of

Cairns, John

Calcitonin

Calcitonin-gene-related peptide (CGRP)

Calcium (Ca²⁺), in RNA structures

Calculation, model building and

Calmodulin

structure of

Calmodulin-binding peptide

Calorie

C_α. See Alpha carbon atom

cAMP. See Adenosine 3′,5′-cyclic monophosphate

cAMP receptor protein (CRP)

allosteric effects of

in combinatorial control

gene transcription and

lac operon and

structure of

Campbell, Allan

cAMP-responsive element-binding protein (CREB)

Campto. See Irinotecan

Camptothecin

Cancer

chemotherapy for

genotoxic compounds

microRNAs in development of

mismatch repair and

mutations in

telomere length and

topoisomerase inhibition for

Cap-binding complex (CBC)

Capecchi, Mario

Capping, of mRNA

during transcription

Capreomycin, translation inhibition by

Carbanion

Carbon, valence of

Carbonyl bond

Carbonyl group, carbon atom of

Carboxyl group

resonance of

Carboxyl terminus

Carcinogens

Ames test for

Carroll, Sean

CASP. See Critical Assessment of Protein Structure Prediction

Catabolite repression

Catalysis

DNA ligase and

enzymes for

principles of

life requirement of

LUCA and

Catalysts

biological

biological reactions and

enzymes. See Enzymes

RNA as

Catalytic RNAs. See Ribozymes

Cate, Jamie

Catenanes

CATH database. See Class, Architecture, Topology, and Homologous superfamily database

Caudal

CBC. See Cap-binding complex

CCR5 protein

CD4

CD spectroscopy. See Circular dichroism spectroscopy

cDNA library

with epitope tags

with GFP gene

cDNAs. See Complementary DNAs

Cech, Thomas

Celera Corporation

Cell cycle

mitosis in

origin firing in

Cell theory

Cell-cell signaling, in development

Cells

asymmetric division of

division of

epigenetic state after

histone modification and

early studies of

nucleotide energy role in

proteome of

specialization of

structures of

transcription factor programming of

Cellular function

RNAs and

transcriptomes and

Centimorgans (cM)

Central dogma of information flow

functional RNAs in

messenger RNA in

I-5

ribosomal RNA in

transfer RNA in

Centromere

Centromere-binding proteins

Centrosome

in prophase

structure of

CFTR. See Cystic fibrosis transmembrane conductance regulator

CFTR

cGMP. See Guanosine 3′,5′-cyclic monophosphate

CGRP. See Calcitonin-gene-related peptide

Chain topology diagram

Chaperones, in protein folding

Chaperonins, in protein folding

Chargaff, Erwin

Chargaff’s rules

Chase, Martha

Chemical basis of information molecules

chemical bonds

electrons in

energy transfer in

molecular behavior and

quantum mechanical terms of

chemical building blocks

of nucleic acids

postsynthetic changes

of proteins

structure with

chemical reactions

catalysts in

laws of thermodynamics

mechanism and speed of

of phosphodiester bonds

pH and ionization

buffers

Henderson-Hasselbalch equation

hydrogen ion concentration

stereochemistry

biological selectivity

proteins and nucleic acids

three-dimensional arrangements

weak chemical interactions

hydrogen bonds

hydrophobic effect

macromolecule interactions and

noncovalent interactions

structure stabilization with

van der Waals forces

Chemical bonds. See Bonds, chemical

Chemical modification interference

Chemical protection footprinting

Chemical reactions. See Reaction, chemical

Chemical shifts, in NMR

Chemistry. See Prebiotic chemistry

Chemotherapy

Chen, Irene

Chi sequence

Chiasmata

Chimpanzees

evolution of

humans and

ChIP. See Chromatin immunoprecipitation

ChIP-Chip technique

ChIP-Seq technique

Chiral center

Chiral molecule

biological selectivity for

proteins and nucleic acids as

Chitin-binding domain

Chloramphenicol

resistance to

translation inhibition by

Chloride channel protein, misfolding of

Chloroplast DNA (cpDNA)

Chloroplasts

evolution of

Cholera

Chromatids, sister pair of

Chromatin

accessibility of

bromodomain proteins and

chromodomain proteins and

deacetylation in

epigenetic inheritance of

filament of

solenoid model of

zigzag model of

forces in

forms of

histone tails and

modification of

histone variants and

hypersensitive sites

loops and coils of

nucleosome repositioning with

pre-mRNA splicing and

structure modulation

transcription activator and

transcription and

Chromatin condensation

SMC proteins in

Snf proteins in

Chromatin immunoprecipitation (ChIP)

Chromatin remodeling complexes

bromodomains and

classes of

control of

epigenetic state and

histone code

mechanisms of action

nucleosome repositioning with

subunits of

Chromatography

affinity. See Affinity chromatography

for protein purification

Chromodomains

Chromosomal replicases

beta sliding clamps and

in eukaryotes

Chromosomal scaffold

Chromosome inversion mutations

Chromosome theory of inheritance

gene location

linked gene segregation

recombination and unlinking of alleles

recombination frequency

Chromosome translocation mutations

Chromosomes

abnormal

fusion gene with

mutations and

artificial

bacterial. See Bacterial artificial chromosomes

human. See Human artificial chromosomes

yeast. See Yeast artificial chromosomes

autosomes

bacterial

behavior of

centromere

contents of

dimeric, with replication fork repair

duplication of

early studies of

of eukaryotes

exons

forms of

function of, genomic sequences and

fusions of

in G₁ phase

in G₂ phase

gene location of

gene silencing and

in genome

homologous

independent assortment of

unlinking of

introns in

inversion of

length of

linkage analysis and

maintenance of

in meiosis

in mitosis

mutations and

nondisjunction

rearrangements of

recombination of

in S phase

scaffold proteins in

segregation of

sex. See Sex chromosomes

size of

in somatic cells

structure of

chromatin filament

linker histone

loops and coils of

regulation of

telomeres

transposition of

viral

W

X. See X chromosome

Y. See Y chromosome

Z

Chronic wasting disease

CIal

I-6

Ciprofloxacin (Cipro)

reversible inhibition by

topoisomerase inhibition by

Circular dichroism (CD) spectroscopy, secondary protein structure and

CIRV

Cis isomer

isomerases and

of polypeptide chains

Cisplatin

Citrulline, arginine auxotrophs and

Clamp loader, of Pol III holoenzymes

DNA replication and

Clark, A. John

Class, Architecture, Topology, and Homologous superfamily database (CATH) database

Clay

lipid vesicles and

prebiotic evolution role of

Cleavage and polyadenylation specificity factor (CPSF-73)

Cleaver, James

Clindamycin, translation inhibition by

Cloning vectors

amplification with

bacterial artificial chromosomes

in DNA library creation

DNA ligase and

electroporation of

expression vectors

gene insertion into

pBR322

plasmids

screenable markers for

selectable markers for

for site-directed mutagenesis

transformation of

yeast artificial chromosomes

Closed complex, in transcription

structural changes and

Closed-circular DNAs

helical turns in

linking number for

relaxed

supercoiling of

thermodynamic straining of

topoisomers

underwinding of

Clustered, regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR/Cas)

for somatic gene therapy

cM. See Centimorgans

CMG complex

Coactivators

for transcriptional regulation

Coalescent theory

Coding strand, in translation

CODIS. See Combined DNA Index System

Codominance

Codon bias

Codon family

Codons

amino acids coded by

definition of

evolution of

experiments cracking

protein synthesis by defined synthetic RNA polymers

protein synthesis by random synthetic RNA polymers

validation in living cells

gaps between

indel mutations and

overlapping of

start

5′-AUG

in translation initiation

stop

in translation termination

triplets forming

tRNA recognition of

mutation suppression

start and stop codons

wobble in

variant

Coelenterates

Coenzyme A

Coenzyme B₁₂

Coenzymes

Cofactors

adenosine in

for DNA ligase

enzymes and

Cohen, Stanley

Cohesin

Coiled-coil motif

Cointegrate

Collagen mutations, protein misfolding in

Collins, Francis

Column chromatography, for protein purification

Combinatorial control of gene expression

in eukaryotes

differentiation

GAL gene

heterodimer mixtures

mating type switch

Combined DNA Index System (CODIS)

Comparative genomics

Competition, in natural selection

Competition inhibition, of enzymes

Complementary DNAs (cDNAs)

building library of

with epitope tags

with GFP gene

preparation of

in transcriptome analysis

Complete medium

Complex transposons

Complexity, of living systems

Composite transposons

Computational biology

protein folding

protein function

genome composition

sequence relationships

structural relationships

Computational protein design

Condensin

Conformational flexibility

of enzymes

of proteins

Conjugate base

Consensus sequences

Conservative DNA replication

Constitutive gene expression

Constructive interference

Contigs

in Human Genome Project

Cooperativity

with homotropic allosteric enzymes

Copper (Cu²⁺), as cofactor

Core histones

Core promoter

Corepressors

Corey, Robert

Correlation spectroscopy (COSY)

Correns, Carl

Corynebacterium diphtheriae

COSY. See Correlation spectroscopy

Coumarins

Coumermycin A1

Covalent bonds

bond angle of

with enzyme functional group

with irreversible inhibitor

mechanisms of

in polypeptide chains

resonance of

strength of

valence in

Covalent modifications

of histones

posttranscriptional regulation by

in protein function regulation

of synthesized proteins

Cozzarelli, Nicholas

cpDNA. See Chloroplast DNA

CPE. See Cytoplasmic polyadenylation element

CPE-binding protein (CPEB)

CpG sequences

CPSF-73. See Cleavage and polyadenylation specificity factor

Craigie, Bob

CREB. See cAMP-responsive element-binding protein

Creighton, Harriet

Cre-lox

in biotechnology

Creutzfeldt-Jakob disease

Crick, Francis

CRISPR/Cas. See Clustered, regularly interspaced short palindromic repeats/CRISPR-associated proteins

Critical Assessment of Protein Structure Prediction (CASP)

I-7

Crixivan. See Indinavir

Cro protein

Crossing over, allele unlinking with

Cross-linking

of histones

of nitrogen mustards

Cross-pollination

Cross-species hybridization

CRP. See cAMP receptor protein

Cruciform structures

with underwinding

CSF1PO

CTD

C-terminus

Cut-and-paste transposition

in eukaryotes

insertion sequences in

cyclic AMP. See Adenosine 3′,5′-cyclic monophosphate

Cyclin-dependent protein kinases

Cyclobutane ring

photoreactivation of

Cycloheximide, translation inhibition by

Cycloserine, translation inhibition by

Cysteine (Cys, C)

ADP-ribosylation of

chemical properties of

in protein folding

in secondary structures

structure of

Cystic fibrosis

protein misfolding in

Cystic fibrosis transmembrane conductance regulator (CFTR)

Cytidine

nomenclature for

structure of

Cytidine deaminases

Cytidylate

nomenclature for

structure of

Cytogenetics

meiosis

mitosis

sex determination in

Cytokinesis

Cytology

cell structures

genetics union with

meiosis

mitosis

sex determination in

Cytoplasmic inheritance

Cytoplasmic membrane

bacterial DNA and

Cytoplasmic polyadenylation element (CPE)

Cytosine (C)

base pairing with

in base triples

deamination of

in DNA structure

early studies of

melting temperature and

methylation of

modification of

nomenclature for

oxidative damage to

RNA editing of

in RNA structure

substitution of

structure of

Cytoskeletal fiber, structure of

D. See Aspartate

D3S1358

D5S818

D7S820

D8S1179

D13S317

D16S539

D18S51

D21S11

D form enantiomers

Da. See Daltons

Dahiyat, Bassil

Dalfopristin, translation inhibition by

Dalgarno, Lynn

Daltons (Da)

Dam methylase

Darwin, Charles

exploration and observation of

on natural selection

pangenesis

world of

Darwinian evolution

Daughter strands, in DNA replication

direction of

semiconservative

DCC. See Dosage compensation complex

DDE motif

DDI. See Dideoxyinosine

ddNTPs. See Dideoxynucleoside triphosphates

de Lange, Titia

de Vries, Hugo

Deacetylation, of histones

DEAD box

Deamination

nitrous acid induced

of nucleotides

Death, of living systems

Decapentaplegic

Deduction, hypothesis and

Deductive reasoning

Deep sequencing

Degenerate code

Deinococcus radiodurans

evolution of

recombination in

Deletion analysis

Deletion mutations

large

Denaturation

Denisovans

Deoxyadenosine

nomenclature for

structure of

5′-Deoxyadenosylcobalamin (coenzyme B₁₂)

Deoxyadenylate

nomenclature for

structure of

Deoxycytidine

nomenclature for

structure of

Deoxycytidylate

nomenclature for

structure of

Deoxyguanosine

nomenclature for

rotation of

structure of

Deoxyguanylate

nomenclature for

structure of

Deoxynucleoside triphosphates (dNTPs)

DNA polymerase I binding to

incorrect

in DNA replication

tautomers in

in PCR

in Sanger method

Deoxyribonucleic acid. See DNA

Deoxyribonucleotides

Deoxyribose

enantiomers of

2′-Deoxy-d-ribose

Deoxythymidine

nomenclature for

rotation of

structure of

Deoxythymidylate

nomenclature for

structure of

Dephosphorylation, of amino acids

Depurination

DeRisi, Joe

Descartes, René

Development

gene regulation in

asymmetric cell divisions in

cell-cell signaling

homeotic genes

maternal genes in

segmentation genes

stem cells

of living systems

regulatory protein cascades in

stages of

Developmental biology

Dextrorotatory (d form) enantiomers

Dicer

structure of

Dickerson, Richard

Dickerson dodecamer structure

Dideoxy chain-termination method. See Sanger DNA sequencing procedure

Dideoxyinosine (DDI), for HIV infection

Dideoxynucleoside triphosphates (ddNTPs), in Sanger method

Differentiation

combinatorial control of

of muscle

of stem cells

Diffraction pattern, in X-ray crystallography

Dihydrouridine

Dimer

I-8

Dimeric chromosomes, with replication fork repair

Dimethylarginine

Dimethyllysine

Dimethylsulfate (DMS), DNA and

DinI

Dintzis, Howard

Diphtheria toxin, translation inhibition by

Diploid organisms

chromosomes of

genome of

Direct repair

Directed evolution, of Escherichia coli

Directionality

of DNA

of helicases

Discovery

hypothesis and

scientific approach to

with scientific method

Dispersive DNA replication

Dissociation constant (K_d)

of DNA-binding proteins

in protein-ligand interaction

representative

distal-less

Distributive synthesis

Disulfide bonds

Dmc1

DMS. See Dimethylsulfate

DNA

alterations in

alkylating agents

Ames test for

chemotherapy and

errant replication and recombination

hydrolysis

oxidative damage

solar radiation

SOS response and

TLS polymerases and

bacterial. See Bacterial DNA

beta clamp protein binding of

biological information and

chemical building blocks of

modification of

chemical synthesis of

for chromosome maintenance

closed-circular. See Closed-circular DNAs

directionality of

discovery of

early studies of

elastic properties of

encoding by

evolutionary relationships with

exons

function of

gel electrophoresis of

heredity and

human. See Human genome

information flow and

central dogma of

functional RNAs in

messenger RNA in

ribosomal RNA in

transfer RNA in

introns in

LUCA and

mitochondrial. See Mitochondrial DNA

mutations in. See Mutations

noncoding

Northern blotting of

nucleosomes and accessibility of

nucleotides of

recombinant. See Recombinant DNA

RNA polymerase binding to

RNA synthesis from

synthesis of

automation of

damaged template in

in DNA cloning

PP_i release in

from RNA

Sanger method and

topoisomerases in

transcription factor binding to

separate domains for

structural motifs for

translocation of

with helicases

with translocases

unwinding of, helicases in

uptake of

viral

weak chemical bonds and

DNA adenine methyltransferase methylase

DNA cloning

alteration of

with baculoviruses

development of

DNA libraries for

DNA ligase in

expression of

genetically modified organisms

GFP

ligation reaction

PCR amplification of

restriction endonucleases in

Sanger method with

steps in

vectors for

amplification with

bacterial artificial chromosomes

DNA ligase

pBR322

plasmids

restriction endonucleases

yeast artificial chromosomes

DNA compaction

chromatin filament

solenoid model of

zigzag model of

enzymes for

bacterial type II topoisomerases

eukaryotic topoisomerases

SMC proteins

topoisomerase I

topoisomerase II

histone organization for

chaperones for

histone tail modification

histone tails and

internucleosome connections

repeating units for

variants and

wrapping of

linker histone in

loops and coils of

nucleosomes for. See Nucleosomes

plectonemic supercoiling for

repeating units for

solenoidal supercoiling for

DNA footprinting

DNA genotyping

DNA glycosylases

DNA gyrase

distinct functions of

inhibition of

negative supercoils with

subunits of

DNA helicases

ATP-coupling stoichiometry with

directionality of

oligomeric state of

processivity of

at replication fork

step size of

superfamilies of

T7

DNA libraries

Neanderthal

DNA ligase

cloning vectors and

cofactors for

discovery of

in DNA cloning

in DSB repair

reaction withf

at replication fork

DNA looping

DNA methylases

DNA microarrays, for gene function

DNA nanotechnology

DNA nucleases

DNA photolyase

DNA polylinkers

DNA polymerase

antimutator

of bacteriophage T7

discovery of

in DNA replication

efficiency of

errors with

of Escherichia coli

exonuclease activity of

I-9

indel mutation and

in PCR

point mutation and

processivity of

replication fork and

reversible inhibition of

in reversible terminator sequencing

Sanger method and

in semidiscontinous replication

structures of

telomeres. See Telomeres

from Thermus aquaticus

TLS

DNA polymerase I (Pol I)

classification of

closed form of

discovery of

for DNA cloning

in DNA elongation

dNTPs and

domains of

3′→5′ exonuclease

5′→3′ exonuclease

function of

insertion site for

open form of

post-insertion site for

primed template for

primer strand for

primer terminus for

at replication fork

structure of

base pairing in

dNTP binding to

metal ions in

template strand for

DNA polymerase II (Pol II)

discovery of

SSB interaction with

DNA polymerase III (Pol III)

beta sliding clamps and

discovery of

DNA synthesis by

in E. coli

holoenzyme

mismatch repair with. See Mismatch repair

structure of

χ subunit of

DNA polymerase IV (Pol IV), discovery of

DNA polymerase V (Pol V)

discovery of

proteolytic cleavage of

SSB interaction with

DNA polymerase α (Pol α)

DNA polymerase β subunit, of Escherichia coli

DNA polymerase δ (Pol δ)

DNA polymerase ε (Pol ε)

DNA probe

for DNA microarray

hybridization of

DNA repair

base excision

direct

energy use for

evolution of

mechanisms of

mismatch

nucleotide excision

point mutations in

recombination. See Recombination repair

SMC proteins in

SOS response

transcription coupling to

translesion synthesis

DNA replication

accuracy of

β sliding clamps and

bidirectional

clamp loader and

conservative

daughter strands in

direction of

semiconservative

dispersive

distributive synthesis

DNA damage with

DNA polymerase in. See DNA polymerase

elongation in

epigenetic state after

histone modification in

initiation of

control of

eukaryotic origins

replication fork assembly

initiator protein for

insertion site for

lagging strand

leading strand

mechanism for

nick translation in

origin of

requirement for

post-insertion site for

primed template for

primer strand for

primer terminus for

processive synthesis

proofreading

replication fork. See Replication fork

replication genes for

semiconservative

semidiscontinous

site-specific recombination and

supercoiling and

template strand for

termination of

in E. coli

in eukaryotes

θ-form

DNA replication fork. See Replication fork

DNA sequencing

assembly of

454 sequencing

ion torrent

new generations of

reversible terminator sequencing

Sanger method for

shotgun sequencing

single molecule real time sequencing

steps for

for transcriptome analysis

DNA strand invasion

DNA structure

A-form of

annealing of

bases of

methylation of

bending in

B-form of

Chargaff’s rule

chirality of

composition of

cruciform structures in

with underwinding

denaturation of

discovery of

double helix. See Double helix

electronic interactions in

four-stranded

hairpin structures in

helical forms of

hybridization of

hydrolysis of

inverted repeats in

ionic bonds in

mirror repeat in

mutations in

nomenclature for

palindromes in

pentose sugar of

polarity of

relaxed

sugar pucker in

supercoiling of

discovery of

plectonemic

replication and

solenoidal

transcription and

three-dimensional

three-stranded

topology of. See Topology

underwinding of

cruciform structure with

linking number for

topoisomerases in

water molecules in

weak chemical interactions in

Z-form of

DNA topoisomerase. See Topoisomerases

DnaA

classification of

domains of

origin binding of

DnaB helicase

assembly of

Pol III holoenzyme and

translocation of

DNA-binding proteins

discovery of

electrostatic interactions with

function of

genetic coding for

hydrogen bonding with

hydrophobic effect with

I-10

nonspecific

nonspecific vs. specific

salt concentration and

single-stranded. See Single-stranded DNA-binding protein

specific

in yeast two-hybrid analysis

DNA-binding transcription activators

DNA-dependent RNA polymerase

DnaG primase

DnaJ

DnaK

DNA-PKcs

DNase I

dNTPs. See Deoxynucleoside triphosphates

Dobzhansky, Theodosius

Dodecamer structure

Domains

exons and

of protein structures

quaternary structures and

supersecondary structural elements in

with α helix

with β-α-β motif

containing β sheet

Dominance

codominance

incomplete

Dominant allele

Donor site, in transposition

Dosage compensation

Dosage compensation complex (DCC)

Double bond

in polypeptide chain

rotation around

Double helix

A-form of

annealing of

antiparallel

B-form of

confirmation of

denaturation of

directionality of

discovery of

DNA as

geometries of

hydrogen bonds in

left-handed

periodicity of

right-handed

stability of

UV light absorption and

Z-form of

Double-strand break (DSB)

danger of

formation of

meiotic recombination at

mitotic recombination at

nonhomologous end joining for

processing of

recombination repair of

replication fork

collapsed

stalled

source of

Double-strand break repair (DSBR)

danger of

in meiosis recombination

in mitotic recombination

for replication fork collapse

Double-stranded DNA (dsDNA)

dissociation constant for

linking number for

protein binding to

from retroviruses

viruses

Double-stranded RNAs

Doxorubicin (Adriamycin)

Dröge, Peter

Drosha

Drosophila melanogaster

alternative splicing and

basic information on

development in

homeotic genes

maternal genes in

regulatory protein cascades in

segmentation genes

stages of

differentiation in

DNA of

life cycle of

as model organism

mRNA transport in

mutations in

sex-linked genes in

transcription factors in

DSB. See Double-strand break

DSBR. See Double-strand break repair

Dscam gene

dsDNA. See Double-stranded DNA

Dulbecco, Renato

Dunaway, Marietta

Duplication mutation

Dynan, William

Dynein

E. See Glutamate

E site, of ribosomes

Echols, Harrison

EcoRI

EcoRV

Edeine, translation inhibition by

Editosome

eEF1a

eEF1b

eEF2

Effectors

EF-G

translocation role of

EF-Ts

EF-Tu

Egelman, Ed

eIF1

eIF1A

eIF2

phosphorylation of

eIF3

eIF4B

eIF4F complex

eIF5

eIF5B

EJC. See Exon junction complex

Elastic properties, of DNA

Electric dipole moment

in α helix

Electron density map

Electron microscopy

diffraction in

of SMC proteins

Electronegative atoms

Electronegativity

in chemical reaction

mechanisms of

electric dipole moment and

energy release and

in hydrogen bonds

Electrons

chemical reaction mechanisms

in covalent bonds

in ionic bonds

molecular behavior and

in valence bond model

Electrophiles, in chemical reaction mechanisms of

Electrophoresis. See Gel electrophoresis;

Sodium dodecyl sulfate–polyacrylamide gel electrophoresis

Electrophoretic gel, for Sanger automation

Electrophoretic mobility shift assay (EMSA)

Electroporation

Electropositive atoms

Electrostatic interactions, with DNA-binding proteins

Electrostatic surface representation

Ellipticine

Elongation

in transcription

bacterial

posttranscriptional regulation of

in translation

elongation factors in

GTP binding and hydrolysis in

inhibitors of

substrate positioning and incoming tRNA role in

Elongation complex

Elongation factors

bacterial

eukaryotic

Embryonic stem cells

EMSA. See Electrophoretic mobility shift assay

En protein

Enacyloxins, translation inhibition by

Enantiomers

of amino acids

of nucleotides

ENCODE

End replication problem

overview of

telomeres and

Endo, Y.

Endonucleases

AP

homing

restriction. See Restriction endonucleases

I-11

Endoplasmic reticulum (ER)

protein targeting modifications in

structure of

Endosymbiotic relationships

Energy

chemical bond changes and

for DNA repair

enzymes and

equilibrium and

first law of thermodynamics and

for living systems

acquisition of

LUCA and

for mismatch repair

nucleotides and

phosphodiester bonds and

for translation

Engrailed

Enhanceosomes

Enhancers

Entropy

env gene

in HIV

Envelope, for living systems

Enzyme kinetics

general rate constant

initial velocity

maximum velocity

Michaelis-Menten equation and

pre-steady state in

steady state in

turnover number

Enzymes

activation energy and

active sites on

allosteric. See Allosteric enzymes

apoenzymes

in biomolecule breakdown

for biotechnology

in biotechnology

for catalysis

DNA ligase

principles of

coenzymes

cofactors with

conformational flexibility of

for DNA compaction. See DNA compaction

for DNA underwinding

evolution of

genetic encoding of

genetic transmission of

group transfers with

holoenzymes

hydrogen atoms and

inhibition of

noncovalent binding energy and

for nonhomologous end joining

overview of

prosthetic group in

for recombination repair

regulatory

restriction. See Restriction endonucleases

RNA. See also Ribozymes

specificity of

substrates for

EP retrotransposons. See Extrachromosomally primed retrotransposons

Epigenetic inheritance

of chromatin state

Epistasis

Epitope tag

of GFP gene

for protein-protein interactions

Equilibrium

with enzymes

free energy and

Equilibrium constant (K_eq)

Equilibrium dialysis

Equilibrium expression

ER. See Endoplasmic reticulum

eRF1

eRF3

Erythrocytes, sickle-cell anemia and

Escherichia coli

amino acid biosynthesis in

basic information on

β sliding clamps of

chromosomal replicase and

cAMP receptor protein of

directed evolution of

DNA of

DNA polymerase III in

DNA synthesis by

holoenzyme

structure of

DNA polymerase β subunit of

DNA polymerases of

DnaJ and DnaK chaperones of

genome of

GroEL/GroES chaperonins of

lactose metabolism in

lactose operon in

methylation system of

as model organism

NER in

oriC

activation of

positive regulation in

radiation resistance of

recombinant proteins from

replication fork of

replication initiation in

replication termination in

sigma factors of

SSB of

topoisomerases of

ESEs. See Exonic splicing enhancers

ESSs. See Exonic splicing silencers

EST. See Expressed sequence tag

Etoposide (Etopophos)

Euchromatin

Euclid

Eukaryotes

BER in

biological information flow in

cell cycle of

cellular structure of

chloroplasts of

chromosomes in

centromere

forms of

maintenance of

size of

cohesins in

condensins in

defective mRNA detection in

DNA replication in

origins for

termination of

elongation factors of

evolution of

glycosylation in protein targeting of

histones of

homologous recombination in

initiation factors of

mitochondria of

mRNA and ribosomal subunit attachment in

NER in

promoters of

replication fork in

chromosomal replicases

CMG complex

MCM complex

PCNA

Pol α

proteins in

RFC

RPA

RPC

retrotransposons in

ribosomes in

RNA degradation in

SMC proteins in

transcription in. See Transcription

transposons in

Evans, Martin

eve gene

Even-skipped

Evo-devo

Evolution

adenosine-containing compounds

branching

Darwinian

of Deinococcus radiodurans

directed, of Escherichia coli

of DNA repair

of enzymes

evo-devo and

genome assessment and

accelerated

outgroups

phylogenetic trees

human. See Human evolution

of introns

Lamarckian

last universal common ancestor

of microorganisms

mutations in

by natural selection

primary protein structure and

process of

I-12

protein structure and

ribosomal RNA and

of ribosomes

thymine in

of translation machinery

of transposons

immunoglobulin genes

interplay of

viruses and introns with

of viruses

transposons and

Exo1

Exon junction complex (EJC)

mRNA degradation and

Exonic splicing enhancers (ESEs)

Exonic splicing silencers (ESSs)

Exons

assembly of

domains and

proportion of

trans-splicing of

Exonuclease I

Exonuclease III

Exonuclease IX

Exonucleases

3′→5′

5′→3′

Exosome

Exothermic bonding

Exploration, observation and

Exportins

Expressed sequence tag (EST), in Human Genome Project

Expression vectors

Extrachromosomally primed (EP) retrotransposons

eukaryotic

F. See Phenylalanine

F₁ generation

with incomplete dominance

with linked genes

unlinking of

in single-factor crosses

in two-factor crosses

F₂ generation

with linked genes

unlinking of

in single-factor crosses

in two-factor crosses

F₃ generation, in single-factor crosses

F plasmid

Factor VIII

FAD. See Flavin adenine dinucleotide

Fatty acid, biosynthesis of

FBF-1

Feedback loops, in gene expression

Ferris, James

FGA

Fire, Andrew

First law of Mendelian genetics

First law of thermodynamics

Fitch, Walter

5′-AUG initiation codon, tRNA for

5′-cap

addition of

formation of

ribosomes and

Flagellin

Flavin adenine dinucleotide (FAD)

adenosine role in

Flemming, Walther

fljA gene

fljB gene

Flowers

incomplete dominance in

Mendel’s study of

dominant and recessive traits

independent assortment

Flp

in biotechnology

Flp recombination target (FRT)

Flu outbreak

Fluorochromes

Fluorophore

fMet-tRNA^fMet. See N-formylmethionyl-tRNA^fMet

Fold Classification Based on Structure-Structure alignment of Proteins (FSSP) database

Foldit program

Forensic medicine, DNA genotyping

Fork regression

Fossils

454 sequencing

Four-helix bundle

Fourier series, in X-ray crystallography

Four-stranded DNA structures

Fractionating resin, for protein purification

Fragile X syndrome

Fragile X-E syndrome

Frameshift mutations

Franklin, Rosalind

Free energy (G)

Free-energy change (ΔG)

in ATP hydrolysis

binding

biochemical standard

catalysts and

in DNA replication

in enzyme-catalyzed reaction

of high-energy bond hydrolysis

in protein folding

Free-energy funnel

Friedreich’s ataxia

FRT. See Flp recombination target

Fructose 6-phosphate

Fruit flies. See Drosophila melanogaster

FSD1

FSSP database. See Fold Classification Based on Structure-Structure alignment of Proteins database

ftz gene

Functional RNAs

RNA polymerase III and

β-Furanose form

Fusidic acid, translation inhibition by

Fusion gene

Fusion protein

cloned genes and

for localization

G. See Glycine; Guanine

G. See Free energy

ΔG. See Free-energy change

ΔG′°. See Biochemical standard free-energy change

ΔG°. See Standard Gibbs free-energy change

G₀ phase

G₁ phase

G₂ phase

G protein–coupled receptors (GPCRs)

gag gene

Gag protein

Gain-of-function mutations

Gal3p

Gal4 protein (Gal4p)

Gal80p

GAL genes

combinatorial control of

galactose and

gal operon. See Galactose operon

Gal promoter

Gal repressor

Galactose (gal) operon

β-Galactosidase

with BACs

lac operon and

promoter and

as protein tag

Galactoside permease protein

β-Galactosides

Galileo Galilei

Gamete cells

allele pairs and

chromosomes in

independent segregation of

unlinking of

formation of

gene assortment in

linked genes in

meiosis of

mutations and

Gamma crystallin, domains of

Gamma rays

double-strand breaks and

recombination and

Gamma turn

γδ resolvase

Gap genes

Gap repair

Garden pea

inheritance in

traits of

Garrod, Archibald

I-13

Gates, Julie

ΔG_B. See Binding energy

GCN4

Gcn5

Gel electrophoresis

of hybrid duplexes

for proteomics

pulsed field

sodium dodecyl sulfate-polyacrylamide. See Sodium dodecyl sulfate-polyacrylamide gel electrophoresis

Gel-exclusion chromatography, for protein purification

Gellert, Martin

Gene dosage compensation

Gene expression

control of

DNA-binding proteins in

exons and

Lac promoter and

methylation and

proteins and

RNA splicing and

RNA structure and

transcriptional regulation in

Gene regulation

activators and repressors controlling RNA polymerase function at promoters

in bacteria. See Gene regulation in bacteria (below)

classical techniques in

combinatorial control

DNA looping

in eukaryotes. See Gene regulation in eukaryotes (below)

eukaryotic compared with bacterial promoters

feedback loops

groups of genes regulated together

microRNAs in cancer development

nucleosomes

posttranscriptional. See Posttranscriptional regulation

separate DNA-binding and regulatory domains of transcription factors

signal integration

with site-specific recombination

transcription factor structural motifs

Gene regulation in bacteria

bacteriophage λ

RNA in

glmS riboswitch

ribosomal proteins

riboswitches

TPP riboswitch

after transcription

transcriptional

amino acid biosynthesis and

CRP

negative

positive

quorum sensing

SOS response

Gene regulation in eukaryotes

combinatorial

differentiation

GAL gene

heterodimer mixtures

mating type switch

in development

asymmetric cell divisions in

cell-cell signaling

homeotic genes

maternal genes in

regulatory protein cascades

segmentation genes

stages of

stem cells

large-scale

AU-rich elements

pre-mRNA splicing

UTRs in

posttranscriptional

alternative splicing

mRNA cleavage sites

nuclear transport

RNA interference

gene silencing

molecular biology with

mRNA degradation

viral gene expression

transcriptional

basic mechanisms of

chromatin structure

coactivators

general transcription factors

positive regulation

transcription activators

transcriptional mechanisms

dosage compensation

enhanceosomes

gene silencing

imprinting

insulators

nonsteroid hormones

steroid hormones

translational control

3′ UTR in

eIF2 phosphorylation in

mRNA degradation rates

upstream open reading frames

Gene silencing

chromosomes and

by microRNAs

by small RNAs

General acid and base catalysis

General rate constant (k_cat)

General transcription factors, for transcriptional regulation

Genes. See also Genome

activation of, with site-specific recombination systems

chromosomal location of

cloning of

alteration of

amplification with

with baculoviruses

cloning vectors in

DNA libraries for

expression of

GFP

steps for

cutting of

CRISPR/Cas for

transcription activator-like effector nucleases for

zinc finger nucleases for

discovery of

encoding by

epigenetic control of

examination of

functions of. See also Protein function

absence of

comparative genomics for

computation approaches to

DNA microarrays for

mutations and

synteny

fusion

gap

history of

homeotic

homologs of

horizontal transfer of

immunoglobulin assembly

independent assortment of

linked genes and

unlinking and

insertion of

into cloning vectors

with site-specific recombination systems

interrupted

linked. See Linked genes

localization of

maternal

mutations in

oncogenes

orthologs of

pair-rule

paralogs of

PCR amplification of

phenotype and

population frequency of

programmed conversion of

recombination

replication

reporter

of retroviruses

segment polarity

I-14

segmentation

segregation of

sequencing of

assembly of

454 sequencing

ion torrent

new sequencing methods with

reversible terminator sequencing

Sanger method

shotgun sequencing

single molecule real time sequencing

steps for

sex-linked

transcriptome

transposons and

tumor suppressor

universal

Genetic code

definition of

degeneracy of

deviations from

initiation and termination rule exceptions

mitochondrial tRNAs

evolution of

experiments used in cracking of

protein synthesis by defined synthetic RNA polymers

protein synthesis by random synthetic RNA polymers

validation in living cells

mutation resistance by

origin of life and

rules of

exceptions to

linear protein synthesis

no gaps

no overlap

triplet codons

tRNA in deciphering of

adaptor function

mutation suppression

start and stop codons

structure

wobble in

Genetic crossover

Genetic disorders

genome sequencing and

homologous recombination and

linkage analysis

motor protein defects and

mutations and

indel

point

NER and

protein misfolding in

RNA splicing and

somatic gene therapy for

Genetic drift

Genetic engineering. See Biotechnology

Genetic history

Africa start of

common ancestor

genome comparisons for

Genetic information

DNA as carrier of

enzymes and

minimum requirements of

transmission of

Genetic maps, with recombination frequency

Genetic reassortment of RNA

Genetically modified organisms

Genetics

cytology union with

history of

Mendelian. See Mendelian genetics

mutations. See Mutations

terminology for

Genome

editing with recombination

of Escherichia coli

genetic history of

of Haemophilus influenzae

of Homo neanderthalensis

of humans. See Human genome; Human Genome Project

minimal

outgroups

protein function and

rearrangements of

study of

viral

Genome annotation

comparative genomics

computational approaches to

gene identity

protein and RNA function in

Genome databases

of archaea

of bacteria

of eukaryotes

genetic disorders and

of viruses

Genome sequencing

assembly of

of bacteria

454 sequencing

genetic disorders and

of Haemophilus influenzae

humanity and

of humans. See Human Genome Project

ion torrent

new generations of

reversible terminator sequencing

Sanger method for

automation of

shotgun sequencing

single molecule real time sequencing

steps for

timeline of

Genomic Adam

Genomic imprinting

Genomic library

Genomics

comparative

LUCA and

Genotoxic

Genotypes

DNA fingerprinting of

in single-factor crosses

in two-factor crosses

Georgescu, Roxana

GFP. See Green fluorescent protein

Giant repressor

Gibbs, Josiah Willard

Gilbert, Walter

glmS riboswitch

Gln. See Glutamine

Globin family

GLR1

Glu. See Glutamate

Glucosamine 6-phosphate

Glucose

GAL genes and

lac operon and

Glutamate (Glu, E)

chemical properties of

DNA-binding of

ionic bonds between

methylation of

in protein folding

in secondary structures

structure of

Glutamate dehydrogenase

Glutamine (Gln, Q)

ADP-ribosylation of

chemical properties of

DNA-binding of

in protein folding

in secondary structures

structure of

Glutathione-S-transferase (GST), as protein tag

Glycine (Gly, G)

in β turns

chemical properties of

enantiomers of

in protein folding

Ramachandran plot for

in secondary structures

structure of

Glycosidic bond

free rotation about

hydrolysis of

Glycosylation

in eukaryotic protein targeting

of proteins

Golgi apparatus, structure of

Golgi complex, protein glycosylation in

Goodman, Myron

Gosling, Raymond

Gottesman, Max

Gottesman, Susan

GPCRs. See G protein-coupled receptors

Great library of Alexandria

Greek key motif

Green, Rachel

Green fluorescent protein (GFP)

cDNA library of

cloning of

development of

I-15

for neuron tracing

for protein localization

Greider, Carol

Griffith, Frederick

Griffith, Jack

Grindley, Nigel

gRNAs. See Guide RNAs

GroEL chaperonin

GroES chaperonin

Gross, Carol

Group I introns, self-splicing of

Group II introns, self-splicing of

Group transfers, with enzymes

Growth, of living systems

GST. See Glutathione-S-transferase

GTP. See Guanosine triphosphate

GTP-binding proteins

sequence and

structure of

Guanine (G)

alkylation of

base pairing with

deamination of

DMS and

in DNA structure

early studies of

hydrogen bonding with

melting temperature and

methylation of

modification of

nomenclature for

oxidative damage to

in RNA structure

pairing of

substitution of

rotation of

structure of

in tetraplex DNA

Guanosine

nomenclature for

structure of

Guanosine 3′,5′-cyclic monophosphate (cGMP)

Guanosine triphosphate (GTP)

elongation regulation by

energy storage and release with

Guanylate

nomenclature for

structure of

Guanylyltransferase

Guide RNAs (gRNAs)

Gutell, Robin

Guthrie, Christine

Gyrase. See DNA gyrase

H. See Histidine

HACs. See Human artificial chromosomes

HaeIII

Haemophilus influenzae, genome of

Hairpin structures

in DNA

in RNA

Haldane, J. B. S.

Hall, Traci

Hannon, Greg

Haploid cells

formation of

gametes as

mating types

Haplotypes

migrations in

in mitochondria

on Y chromosome

HapR

HAR1A locus

Harvey, Stephen

HATs. See Histone acetyltransferases

HCN. See Hydrogen cyanide

HCV. See Hepatitis C virus

HDACs. See Histone deacetylases

He, Lin

Heat, chemical bonds and

Heitler, Walter

Helical wheel

Helicases

ATP-coupling stoichiometry with

autoinhibition of

biochemical properties of

directionality of

DNA. See DNA helicases

DNA unwinding with

oligomeric state of

PcrA

processivity of

RecG

RecJ

RecQ

step size of

superfamilies of

T7

in translocation

Helix-loop-helix motif

in lac operon

in transcription factors

Helix-turn-helix motif

in Lac repressor-DNA interaction

in transcription factors

Hemoglobin

pH and

sickle-cell anemia of

structure of

Hemoglobin A

Hemoglobin S

Hemophilia

Henderson-Hasselbalch equation

Henkin, Tina

Hepatitis C virus (HCV)

5′ end–independent translation initiation mechanisms of

miRNA and

Heptad repeat

Hershey, Alfred

Hertwig, Oskar

Heterochromatin

Heterocyclic base. See Bases

Heterocyclic compound

Heterodimer formation, combinatorial control by

Heterooligomer

Heterotropic allosteric enzymes

kinetic properties of

Heterozygotes

in codominance

in incomplete dominance

Hh protein

Hierarchical model, of protein folding

High-mobility group (HMG) proteins

Hin recombinase

HindIII

Hingorani, Manju

His. See Histidine

His₆

Histidine (His, H)

chemical properties of

phosphorylation of

in protein folding

in secondary structures

structure of

Histone acetylase, discovery of

Histone acetyltransferases (HATs)

Histone chaperones

Histone code

Histone deacetylases (HDACs)

Histone modifying enzymes

epigenetic state and

histone code

Histone octamers

crystal structure of

discovery of

DNA organization by

crystal structure of

histone tail modification

histone tails and

histone-fold motif

internucleosome connections

repeating units for

sequence and

underwinding and

variants and

formation of

organization of

tails of

modification of

Histone tails

DNA organization and

modification of

Histone-fold motif

Histones

bromodomain proteins and

chromatin remodeling complexes and

epigenetic state and

histone code

chromodomain proteins and

deacetylation of

DNA transcription and

covalent modification and

histone modifying enzymes and

epigenetic state and

histone code

linker

mRNA for

nucleosome binding with

I-16

organization of

types of

variants of

X chromosome inactivation and

HIV. See Human immunodeficiency virus

HMG proteins. See High-mobility group proteins

HMG-Box

HMLα

HMRa

Hoagland, Mahlon

Hofmeister, Wilhelm

Holley, Robert

Holliday, Robin

Holliday intermediates

in meiosis recombination

processing of

Holliday junction resolvases

Holoenzymes

Pol III. See Pol III holoenzyme

RNA polymerase

Homeodomain motif, in transcription factors

Homeostasis, of living systems

Homeotic genes

Homing endonucleases

Homo erectus

Homo habilis

Homo neanderthalensis

displacement of

evolution of

genome for

genome sequencing of

Homo sapiens. See Human evolution

Homodimer

Homologous chromosomes

Homologous recombination

completion of

in eukaryotes

genetic diversity with

initiation of

intron movement in

during mitosis

programmed gene conversion

Homologs

in meiosis

Homooligomer

Homotrimer

Homotropic allosteric enzymes

kinetic properties of

Homozygotes

in codominance

in incomplete dominance

Hong Kong flu pandemic

Hoogsteen, Karst

Hoogsteen pairing

Hoogsteen positions

Hooke, Robert

Horizontal gene transfer

Hormone response elements (HREs)

House mouse. See Mus musculus

Housekeeping genes

Hox genes

HREs. See Hormone response elements

Hsp40

Hsp70

HTT

HU protein

Huang, Wenhua

Human artificial chromosomes (HACs)

development of

for somatic gene therapy

Human disease, A-2, A-5

Human evolution

from Africa

diversity in

genomic Adam

migration

mitochondrial Eve

Human genome

accelerated evolution in

bonobos and

chimpanzees and

complexity of

components of

exons

haplotypes

humanity and

introns in

repeated sequences in

retrotransposons

simple-sequence repeats

single nucleotide polymorphisms

telomere sequence of

transposons

Human Genome Diversity Project

Human Genome Project

genetic diseases and

linkage analysis and

Sanger method in

start of

timeline for

Human immunodeficiency virus (HIV)

CCR5 protein and

d-peptides for

evolution of

mutation rate of

nuclear transport and

phylogenetics of

protease

as retrovirus

reverse transcriptase of

inhibitors for

reversible enzyme inhibitors for

RNA structure and

transition state analogs for

vaccine for

Human influenza

Human Mediator

Human pandemic of flu

Hunchback activator

Huntington disease

Hybrid

Hybrid duplexes

formation of

gel electrophoresis of

probe of

Hycamtin. See Topotecan

Hydrogen

alcohol dehydrogenase and

in NMR

valence of

Hydrogen bonds

in α helix

in base pairing

in base triples

in β conformation

in DNA double helix

with DNA-binding proteins

nonspecific

specific

enzymes and

in motor proteins

in protein folding

in secondary protein structure

in secondary RNA structure

Hydrogen cyanide (HCN), adenine synthesis from

Hydrogen ion concentration

Hydrolysis

of ATP

Michaelis-Menten kinetics for

of DNA

of glycosidic bond

GTP, elongation regulation by

of high-energy bonds

of nucleotides

of phosphodiester bonds

Hydrolytic cleavage

Hydronium ions

Hydrophobic effect

with DNA-binding proteins

enzymes and

in motor proteins

in protein folding

in RNA secondary structure

Hydrophobic residues

in molten globule model

in protein folding

in supersecondary structures

Hydrophobic stacking

Hydroxide ion

Hydroxylation, of amino acids

5-Hydroxymethylcytosine

5-Hydroxymethyldeoxycytidine

Hypatia

Hypersensitive sites, in chromatin

Hypochromic effect

Hypotheses

deduction and

discovery and

Hypoxanthine

I. See Isoleucine

IF-1

IF-2

IF-3

IGF2

IgG. See Immunoglobulin G

IgM. See Immunoglobulin M

Ile. See Isoleucine

Illumina sequencing

Image reconstruction, in X-ray crystallography

I-17

Imidazole

Imine group

Imino bond

Immunoblots

Immunofluorescence, proteins localization with

Immunoglobulin evolution

Immunoglobulin G (IgG)

Immunoglobulin M (IgM)

Immunoprecipitation

Importins

Imprinting

In situ hybridization

Incomplete dominance

Indel mutations

large

Indinavir (Crixivan)

Indirect immunofluorescence

Induced fit

Inductive reasoning

Influenza virus

Information. See Biological information

Information flow

central dogma of

functional RNAs in

messenger RNA in

regulation of

activators and repressors controlling RNA polymerase function at promoters

combinatorial control

DNA looping

eukaryotic compared with bacterial promoters

feedback loops

groups of genes regulated together

microRNAs in cancer development

nucleosomes

posttranscriptional. See Posttranscriptional regulation

separate DNA-binding and regulatory domains of transcription factors

signal integration

transcription factor structural motifs

ribosomal RNA in

transfer RNA in

Inheritance

of biological information

chromosome theory of. See Chromosome theory of inheritance

deciphering

DNA and

of dominant traits

epigenetic. See Epigenetic inheritance

in garden pea

of linked genes

unlinking of

of recessive traits

Inhibition, of enzymes

Initial model, in X-ray crystallography

Initial velocity (V₀)

of allosteric enzymes

Initiation

of transcription

bacterial

in eukaryotes

of translation

5′ end–independent mechanisms of

amino acid used for

bacterial initiation factors in

bacterial mRNA recruiting of ribosomal subunits

eukaryote initiation factors in

eukaryotic mRNA recruiting of ribosomal subunits

inhibitors of

Initiation codons

5′-AUG

in translation

Initiation complex

bacterial

eukaryotic

Initiation factors

bacterial

eukaryotic

Initiator protein

Inorganic diphosphate

Inorganic phosphate (P_i), energy storage and release with

Inosine

RNA editing of

Inquiry

Insects, recombinant proteins from

Insertion mutations

large

Insertion sequences (IS)

Insertion site

Inspiration

Insulators

Insulin, phosphorylation control of

int gene

Integrase

mechanism of action of

Interactions, of living systems

Internal ribosome entry site (IRES)

International HapMap

International Human Genome Project. See Human Genome Project

Interphase

in meiosis

in mitosis

Interrupted genes

Intervening sequences. See Introns

Intracellular localization, posttranscriptional regulation by

Intrinsically unstructured proteins

Introns

evolution of

origins of

in pre-mRNA

proportion of

in recombination

self-splicing of

group I

group II

Inversion mutations

Inverted repeats

Invirase. See Saquinavir

Ion torrent

Ion-exchange chromatography, for protein purification

Ionic bonds

enzymes and

in macromolecules

in motor proteins

in protein folding

Ionizing radiation (IR), bacterial resistance to

Ions

DNA binding and

in DNA polymerase I

in RNA structure

IPTG. See Isopropyl β-D-1-thiogalactopyranoside

IR. See Ionizing radiation

IRE. See Iron response element

IRES. See Internal ribosome entry site

Irinotecan (Campto)

Iron (Fe²⁺ or Fe³⁺), as cofactor

Iron homeostasis

Iron response element (IRE)

Iron response proteins (IRPs)

Irreversible inhibition, of enzymes

IS. See Insertion sequences

Isoelectric focusing, in two-dimensional gel electrophoresis

Isoenergetic

Isoleucine (Ile, I)

chemical properties of

in protein folding

in secondary structures

structure of

N⁶-Isopentenyladenosine (6-isopentenylA)

Isopropyl β-D-1-thiogalactopyranoside (IPTG)

ISWI chromatin remodeling complexes

Izsvak, Zsuzanna

Jacob, François

JAK-STAT pathway

Janssens, F. A.

Jeffreys, Alec

Johnson, Ken

Johnson, Tracy

Joyce, Gerald

Jurica, Melissa

K. See Lysine

K_a. See Acid dissociation constant; Association constant

Karyopherins

Kasugamycin, translation inhibition by

k_cat. See General rate constant

K_d. See Dissociation constant

kDa. See Kilodaltons

Keeney, Scott

Kelner, Albert

Kendrew, John

I-18

Kennedy disease

K_eq. See Equilibrium constant

Keratin, structure of

Khorana, H. Gobind

Kilocalories per mole

Kilodaltons (kDa)

Kim, Peter

Kim, Sung-Hou

Kimble, Judith

Kinesin

Kinetic isotope effect

Kinetic proofreading

in translation

Kinetics

of enzymes. See Enzyme kinetics

Michaelis-Menten. See Michaelis-Menten kinetics

pre-steady state

of protein folding

steady state

of enzymes

of motor proteins

Kinetochore

Kirromycins, translation inhibition by

Kleckner, Nancy

Klinman, Judith

Klug, Aaron

K_m. See Michaelis constant

Kobayashi, R.

Kolodner, Richard

Kong, Xiang-Peng

Kornberg, Arthur

Kornberg, Roger

Kornberg, Tom

Kossel, Albrecht

Kozak, Marilyn

Kozak sequence

Krüppel repressor

Ku70-Ku80 complex

Kunkel, Tom

Kuru

L. See Leucine

L form enantiomers

Lac promoter, gene expression and

Lac repressor. See Lactose repressor

Lacks, Henrietta

lacl gene

Lactose metabolism

Lactose (lac) operon

catabolite repression

function of

genes in

glucose and

lactose levels and

negative regulation of

operator sequences for

positive regulation of

for recombinant proteins

Lactose (Lac) repressor

discovery of

dissociation constant for

DNA-binding of

function of

gene for

lac operon and

lactose levels and

purification of

lacZ gene

Lagging strand

damaged template in

in DNA replication

trombone model and

Laipis, Philip

Lamarck, Jean-Baptiste

Lamarckian evolution

Lambda phage. See Bacteriophage λ

Lambda repressor

functions of

growth pathway and

infection and

structure of

Landick, Bob

Large-scale gene regulation

AU-rich elements

pre-mRNA splicing

UTRs in

Last universal common ancestor (LUCA)

genetic code of

in tree of life

Law of independent assortment

Law of segregation

Laws of thermodynamics

Lea1

Leader peptide

Leader sequence

Leading strand

damaged template in

in DNA replication

Lebowitz, Jacob

Lederberg, Esther

Lederberg, Joshua

Left-handed double helix

Lehman, Robert

Lenski, Richard

Leptotene subphase

Leucine (Leu, L)

chemical properties of

in protein folding

in secondary structures

structure of

Leucine repeat

Leucine zipper motif

in transcription factors

Levine, Michael

Levinthal, Cyrus

Levinthal’s paradox

Levorotatory (l form) enantiomers

Lewis, Edward B.

LexA

Licthman, Jeff

Life. See Living systems

Ligands

protein function and. See Protein-ligand interactions

riboswitches and

Ligation reaction

Light microscope, diffraction in

Lincosamides, translation inhibition by

LINEs. See Long interspersed nuclear elements

Linkage analysis

Linked genes

in fruit flies

mapping of

nonindependent segregation of

recombination of

frequency of

Linker histone

Linkers

Linking number (Lk)

for closed-circular DNA

DNA gyrase and

for DNA underwinding

superhelical density

topoisomerase I and

topoisomerase II and

twist of

writhe of

Liphardt, Jan

Lipid vesicles

clay and

for living systems

ribozyme groupings in

RNA-containing

Lipoate

Livet, Jean

Living systems

characteristics of

evolution of

last universal common ancestor

origin of

pathways and processes in

requirements for

RNA world hypothesis and

Lk. See Linking number

lncRNAs. See Long noncoding RNAs

Lobban, Peter

Localization, of proteins

London, Fritz

Long interspersed nuclear elements (LINEs)

in retrotransposons

Long noncoding RNAs (lncRNAs)

Loss-of-function mutations

loxP

LUCA. See Last universal common ancestor

Luciferase, in pyrosequencing

Lukyanov, Sergey

Lwoff, André

Lyon, Mary

Lysine (Lys, K)

acetylation of

histone tails and

chemical properties of

deacetylation of, histone tails and

DNA-binding of

in histone

methylation of, histone tails and

in protein folding

in secondary structures

structure of

ubiquitination of

Lysis

Lysogen

Lysogenic pathway

infection and

I-19

Lysosome, structure of

Lytic pathway

infection and

m. See Molecular mass

M. See Methionine

1M7. See 1-Methyl-7-nitroisatoic anhydride

M phase. See Mitosis

Machado-Joseph disease

MacroH2A

Macrolides, translation inhibition by

Mad cow disease

Magnesium (Mg²⁺)

as cofactor

DNA ligase and

in DNA polymerase I

in nucleic acid metabolism

in RNA polymerase

in RNA structures

Major groove of DNA

discovery of

DNA-binding at

in dodecamer structure

Malthus, Thomas

Maltose-binding protein

Manganese (Mn²⁺), as cofactor

Marcu, Ken

Margulies, Ann Dee

Margulis, Lynn

Markov, Georgi

Mason-Pfizer monkey virus

Mass spectrometry (MS), for proteomics

MAT

Maternal genes

Maternal mRNAs

Mating types

combinatorial control of

Matthaei, Heinrich

Matthews, Brian

Maxam, Allan

Maxam-Gilbert DNA sequencing procedure

Maximum velocity (V_max)

irreversible inhibitors and

reversible inhibitors and

Mayo, Steve

McClintock, Barbara

MCM complex

Medawar, Peter

Mediator complex

Mediator proteins

Medium

complete

minimal

1-meG. See 1-Methylguanosine

7-meG. See 7-Methylguanosine

Meiosis

chromosome segregation in

crossing over during

nondisjunction

phases of

process of

sex determination in

SNPs in

Meiotic recombination

completion of

genetic diversity with

initiation of

Mello, Craig

Melting. See Denaturation

Melting point (T_m)

Mendel, Gregor

background on

genetics and

recognition for

Mendelian genetics

exceptions to

codominance

incomplete dominance

linked genes

first law of

garden pea for

history of

rediscovery of

second law of

Menten, Maud

Merodiploid analysis, of lac operon

Meselson, Matthew

Messenger RNA (mRNA)

5′ end–independent initiation mechanisms of

AREs and stability of

capping of

cleavage sites of

degradation of

in processing bodies

rates of

siRNAs and

translational efficiency and

DNA bending and

in DNA library creation

DNA microarray of

gene silencing in

in information flow

localization of

maternal

Mediator complex and

modification of termini of

noncoding regions of

nuclear export of

pre-mRNA splicing and

polycistronic

precursor. See Precursor mRNA

processing of

in proteome

ribosome assembly on

bacterial initiation factors in

bacterial subunit recruitment for

eukaryotic initiation factors in

eukaryotic subunit recruitment for

ribosomes translocation along

RNA polymerase II and

scanning of

small RNAs affecting stability of

splicing of

chromatin structure and

transcription and

stop codons in

structure of

synthesis of

3′-end ofb

translation control by

in transcriptionb

transcription coupling to

translational repressor and

translation-coupled removal of defective

other mechanisms

tmRNA rescue

UTRs translation coordination in

Met. See Methionine

Metabolism

evolution and

LUCA and

Metagenomics

Metal ions

in DNA polymerase I

in RNA structure

Metamerism

Metaphase

in meiosis

in mitosis

Metaphase plate

Methionine (Met, M)

chemical properties of

in protein folding

in secondary structures

structure of

tRNA for

1-Methyl-3-nitro-l-nitrosoguanidine (MNNG)

1-Methyl-7-nitroisatoic anhydride (1M7), RNA structure and

1-Methyladenine

N⁶-Methyladenosine

Methylarginine

Methylation

direct repair of

of DNA bases

histone tails and

of arginine

of lysine

mismatch repair and

of proteins

of RNA bases

5-Methylcytidine

5-Methylcytosine

N⁶-Methyldeoxyadenosine

5-Methyldeoxycytidine

N²-Methyldeoxyguanosine

7-Methylguanine

1-Methylguanosine (1-meG)

7-Methylguanosine (7-meG)

N²-Methylguanosine

Methyllysine

Methyltransferases

2′-O-Methyluridine

I-20

Mi2/NURD chromatin remodeling complexes

Michaelis, Leonor

Michaelis constant (K_m)

allosteric enzymes and

irreversible inhibitors and

reversible inhibitors and

Michaelis-Menten equation

Michaelis-Menten kinetics

of allosteric enzymes