Lewin Benjamin (ed.) Genes IX

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',uorlpJrJrporu

',saspq

009

'surJlord

Dol

66I

'uopoJ

gvn

ur uoruasur'aursdlorr,{4

Js6I

'561

',YNUl

ul uoIlPrIJIpou

-/ots

rE-ors

';o

:redar uolteurquo)ar'uorlJolsrp

[e]nDnrls

ttOS

,tOS ,uorreldqtau

999

'8urdd11y

ralllrp

sJulPruund

logt'ogt-gst

'uortrqrqur

srsaqtu[s

uralord'up,{uorn4

977

'(sleuBrs

Surta8ret

lerurxored)

514

tz9'qJs.L-d

IOZ'0Z-6I'(prorr^

rrqnt

alpurds o1elod)

n154

9€L

'YN(I

!p)

LIIrM uorDerr

'urlprosd

lOtt'

OSt'pue

y51gl

pa8reqrun

',alls

J^UJP

lPuosoqu

I I z

'vNul-ldpudJd

I8I

'pue

vNdl s9I

'uorDunJ

JbEt

'VSI'Jo

uoururJep

alls

ees'

t-OOg'srsaqlu[s'aurpunopnasd

6oI'uoIDunJ

^rolPln8ar

lsss'sss'691'passa:ord

'auoua8

ueunq ur

ItOt

'tOt-ZOt 'sra1sn1r

auaB urqo13 ur

60I-80I

'sa11lue;

aua8 ur

-/gOt

'OOt-gOt

'spuJ

ppep,{:euounlora

z0I

'28'99 ',Jo

uorlrurJJp

ttOS'tOS-tOS'pue

dlquasse

uqnqolSounuur

uerne

sauaSopnas6

8I9

',lueuala

asd

J16r'r6n

'(rotreJ

uorldr:rsuerl rotdela:

auoruoraqd)

g1g4

0Z':sdrd

phage genomes,

rolling

circles a\d,, )87f,

)97-)98

phage

T4, 445448,447f

restarting,

primosome

for,

45 145), 452f,

45)f

semidiscontinuous, 442

single-strand

DNA, 415437, 436f

speed,

381

unidirectional,

37 8-) 80, )7

37 9

cell cycle

condition, 177

Replication-defective transforming

viruses,

558, 558/

Replication

errors

definition

of, 502, 502f

repair

systems, 5ll-5I), 5l2f,513f

Replication eyes

bidirectional vs unidirectional,

)7 8-)7 9,

37 8f

circular replicon,

j79,

)791

definition of, )7 8, 37 8f

measurement of replicon

size and, 18l,

38lf

Replication forks

foci formation,

383-)84, )84f

generation,

of hemimethylated

sequences,

5J8

initiation,

378, )78f

movemenl

detection

of, 379-380,

j79f,

)8Of

estimation of,

l8l

stalled

disassembly,

tus-ter complex and,

45245),451f

from DNA damage, 451452,

452f

reactivation. 45245), 45)f

repair by recombination, 452,

4r2f

replication-repair

pathways

for, 5 I 1-5 I l,

5r2f,517f

ler elements

and,

45245),

453f

Replication forms, creation, at

origin, 44845O,

448f.449f

Replication slippa

ge,

| 2a-125,

125

Replicative transposition

cointegrates and, 531-133,

532f

definition of, 527, 527f

TnA family, 5)4-i)6, 5jrf

Replicons,

37 6-)91 See also specific replicons

circdar, 179,

)79f

definition of, 177

on eukaryotic chromosomes, 381-384,

387f, )84f

extrachromosom al, )

2407

in homologous recombination,

512

Iinear

5' end and,

393-394,194f

vs circular replicons. 178-179.

)781

origins. 377

autoradiography of, 380, 180/

electrophoresis ol,

9-3

80, 37 9

)80f

plasmid

incompatibility and, 421, 42lf

regional controls, 184

rolling circles and, )96-)97

)96f, 197f

size, )8), )8)f

Iermlnus, J / /

Replisome, 429,447

Repression

binding of repressor to more than

one operator and,

1t5-116

definition of, 106

in ligand absence, steroid receptors and,

658, 658/

methylated CpG doublets and, 615

polycomb group proteins

and,824-826, 825f

repressor-operator binding and,

-j

8, 3

oI transcriplion, by histone deacetylation.

808. 808/

Repressors

autogenous control

(autogenic

circuit), 319-720,

)20f, )65-)66, )65f

binding to operator, SlS-316, )13f, )14f

blockage of lytic cycle, )65,365f

competition

with low-affinity sites,

)\7-)t9, )t9f

loop formation, )15-)16,

jl,5f, jl6f

rate

of dissociation from, I I 4

release, inducer

binding and, )14-j15,

)I5f

RNA

polymerase

binding and, 3

simultaneous

at two separate sites,

)15-)t6, )t5f

cleavage

lytic cycle induction

and,36l-32,

)6lf

RecA

protein

activation and, 5 14

conformation, DNA-binding and,, )12, )12f

control

of lac

gene,

704-)05, )05f

by small-molecular inducer, 306-308,

)07f

defective,

constitutive expression

and, 309, 309f

definition

of, 103

dimers

cooperative

binding with operator,

164, )65f

cooperative inter acrions, )67, ) 67

DNA-binding,

lll

equilibrium equation and, )17, 317f

form,36l-362,

)6If

helix-turn-helix motil a\d, )62,

j62f

specificity, helix-turn-helix

motifs and, )6)-364,

)6jf, )64f

DNA-binding sites

half-turn, )62,362f

high-affinity,

jl6-)17

low-affinity, )16-)17

mutations in, )12-)l), )llf

domains,

j6l,

36lf

C-terminal, )61, )6lf

DNA-binding,

j12,3l2f

N-terminal, )6I,36lf

headpiece, )10, )12

histone deacetylases and, 808, 808/

homeodomain

proteins,

660

IPTG

complex binding, I t 5

isolation, 3 I

/ac operon, )07-)08, )07f

monomers

domains of, 3 t0-3 t l, 3 l0/

structure of, ll l, 3l l/

mutations, )09, )12-)\1, lllf

N-terminal domain, )61-)64, 164f

octamer formation, )67-)68, )67f

OR2,

interaction

with

RNA

polyfll€rose at Pnu,

)65-)66,366f

paftitioning

on DNA, ll7

phage

lambda lytic

cascade

and, 159-360

positive

control

mutations, 365-166, 366f

positive

regulator,

)65-)66,

j6rf

promoter-binding proteins,

648-649,

649f

recognition helix, 659

release

direct model of, )14415,315f

equilibrium

model

ol,

]14, )l5f

synthesis, )68, )68f

c,',

gene prevention

of, l7 I

lysogeny

pathway

and, )68-)70,

)69f

tetramenc core

dimers

in,

)11,31lf, )I2f

monomers in, ll l, lI

mutations, )I1,

jllf

repression requirement, I I 0

translational, )24,

j24f

Rereplication, eukaryotic,

licensing factor control

of,

)85-386, 786f, 787

Resolution

breaking and rejoining bonds

in, 536

delinition of,

463, 5)2

Holliday

junction,

463,

464f

Resolution site

(/'eJ

site), 535

Resolvases

definition of, 527, 532

Holliday

junctions

a\d,

)47

4, 47 4f

in TnA transposition, 534-5)6,

5)5f

Response elements

binding,

activation by Iigand binding,656, 656f

definition oI, 641

on metallothionein

gene,

650, 650/

parrnoromrc,

6) /

o) /J

recogniton

specificity of, 658,

658f

by steroid

receptors, 657-658, 657f,658f

recognition, by

activators, 649-65

650f

stetolo,

nalr

slles,

o)/, o)/_r

rds site

(resolution

site), 515

Restriction endonucleases,

DNA cleavage, )940, 40f

Restriction

enzymes, at methylated sites,

632-6)),672f

Restriction fragment

length

polymorphism (RFLP)

delinition of,

58, 58/

disease

genes

and

58-59.

59f

for

genetic

mapping,58-60,

59f

Restriction

maps

CDNA vs

genomic

DNA, 40, 4tl

construction, 56-57

definition of,

40, 40/

tandem

gene

clusters,

I l2-1 Il,

I I3l

Restriction site

polymorphisms,

58,

58/

Reticuloendothelial

system,

220

Retinoic acid, 614,

654f

Retroposons,550-568

classes. 562-564, 5 62f-5

64f

definition of,

55 I

in Drosophila

melanogaster, 561-562,

56lf

LTR-containing,

563

plants,

561

reverse transcriphses, 56j,

56jf

T! elements

yeast,

559-561, 559f-

56lf

Retrotranslocation.

Sed

Reverse translocation

Retrotransposons. See

Retroposons

Retroviruses,

55O-568

budding,

551,553f

copy choice

recombination,

556, 556f

definition

of, I I

DNA, 554, 554l

J enos,

))/

) enos, ))/

rntegranon, >)t.

))/J

integration

into chromosome,

556-557, 557f

gag gene,

T! elements and,

559, 5591

gag

terminariort

codon,

552-553

genes,

coding lor

polyproteins,

552-553, r53f

mRNA, 552

plus

strand

viruses, 554

pol

gene,

elements and, 559,559f

po1

reading frame, 552-55)

repf ication-defective

transforming,

558, 558f

reproductive cycle,

551-552, 551f,

552f

retroposons,

reverse transcriplases,

563, 563f

RNA, 554,

554l

RNA-dependent

transposition

and, 55

RNA

genomes,

555-556

transduction,

of cellular

sequences, 558-559,

558f

translation,

2 I l

Retrovoiruses,

in human

genome,

56)-564,

564f

Reverse

transcriptases

copy choice

recombination,

556, ,56f

definition ol,

552,554

Index 885

group

II intron transposition

reaction and,

7 16-7 r7

I6f

in retroposons,

56), 56)f

RNAase

H activity, 554-555

telomerase, 7

l-7

52, 7 5 lf

Reverse transcription, I0-I2,

I l/

priming,

LINE elements,

566-567, 566f

processed pseudogenes

and,

565, 565f

Reverse translocation,

2)4-235,

234f

RFl, l7l

RF2, t7)

RF3, l7l

RF-C, 445

gene

mutations, I74

RFLP See Restriction

fragment length polymorphism

RFs See Release factors

Rho-dependent terminators,

287, 288,

290, 29Of

29 4

Rho factor

definition of, 287

function, 288-291,

289f, 29Of.

695

gene

mutations, 29O-29

polariry,

289-290

rut srte, 288-289, 289f

transcription termination,

287, 288-29I,

28ef,2e0[

Ribonuclease

E, in bacterial

mRNA

degradation, l4t

Ribonuclease P

(RNAase

P]},707,718

Ribonucleases

(RNAases).

Ribonucleic

acid See RNA

Ribonucleoprotein.

l)), IJ3f

Ribonucleoprotein

enzyme, telomere

synthesis,

75O-752,75tf

Ribonucleoprotein

particles,

l5l, l5lf

Ribosomal

proteins (r-proteins),

synthesis,

autogenous

regulation,

)25-)26,

)25f, )26f

Ribosomal recycling

factor

(RRF),

174, 175f

Ribosomal RNA

(rRNA)

alternative

genes,

base

pairing

with mRNA, in

protein

synthesis

initiation, l6l-162,

l6lf, l62f

deiinition of, l4

functions,

128, 129, 180,

180/

genes,

I l2

interactions, 17

6-177, I77

codon-anticodon

pairing

and, l8l-182,

l8f/

with mRNA,

180

wirh IRNA,

180

length, 778

processing,

small RNAS lor,

699-7

0O, 699f, TOOf

production,

cleavage

events for,

697-699,

698f

repeated

genes,

I 1.1-l

I 5

ribosomal subunits,

175-177,

176f

r-protein autogenous

control

and, J26,

)26f

l6s

conformational

changes

protein

synthesis, l8l,

l8 r/

crystal

structure, 2l I

l' end of, I 80

protein

synthesis, 179-182,180,

l8t/

translation

accuracy

and, 2 I

0-2 I I

185,153

2lS,

peptidyl

transferase

activiry,

182-183,

l8t

285,

I 5l

size of, l28f

structural conf

ormation,

structure, 17 5-177,

17 6f

tandem repeats,

Il2-113,

lllf

Ribosome

active

centers, 177

-179,

178f, 179f

aminoacyl-IRNA

selection,

for A site insertion,

210,210f

bacterial,

protein

synthesis initiation in, 157-I58,

1571,158f

binding

of elongation factors, 170-172, 171f

regulator

blockage ot, )24, )24f

codon-anticodon

base

pairing

and, l9l

control, of RNA

seacondary structrre, 337,

))7f, J)8

eukaryotic, scanning from

5' end,

163-164, l67f

free,

protein

synthesis in, 222,222f

functions,

177, 179-180, lSOf

interaction wirh

IRNA, I 521-155, 154f, 155f

Iarge subunit

peptide

bond formation in, 154-155,

r54f, r55f

55 RNA, 175

5.8S RNA, 175

large suDunlts, t5t, tJtJ

lifecycle

oI, l)4,1)4f

movement

bypassing and, 214-215, 214f

translational

control ar'd,, )24-)25, 324f

mRNA translation, 1

32-1 33,

33f

mutations, I5l

organelle, I 5l

position,

tryptophan control

of, )37-338, ))7f

proteins

r-proteins,

I 5l

protein

synthesis, 152-15),

l53f

rRNAand,179-180,180/

sedimentation rarc oI, lj2-l)j

sites for binding

charged IRNA

P site, I 54, I 54l

A sfte, 154, l54f

structural analysis, I 53

structural conformation, subunit complex formation

and, I8l

subunits

connections between, 17

6-17

initiation factors and, I

57-I 58,

157f,

l58f

peptide

bond formadon in, 154-155, 154f, l5rf,

t75

protein

synthesis initiadon in, 157-158,

r57f, t58f

rRNA

in, 175-177, 176f

)os,176, t76f

50s, t76, t76f

7OS, 17

6-177, 17 6f, t7 8f

size of, 152-15),

l5)f

small, 133, I33/

translation, initiation

site and,

1,36-l)7

translation

accuracy and, 209-211, 21Of

translocation

activation

of,

172

hybrid state modeI,

169-17O, 170f,'17 8

Ribosome-bindin

siIe, | 57,

l 17

Ribosome

stalling, ll6

Riboswitch,

)40, 341

| 4-7 I 5, 7 | 4f

Ribozymes, 707-726

catalytic reactions, 7

ll-7 15, 7 llf-7 l4f

Michaelis-Menten

kinetics

and, 7 13, 7 Bf

riboswitch,

7 l4-7 |

l4f

definition

of, 707

hammerhead

Mg2+ initiation

of catalysis, 719-720,720f

self-clevage, 7 19, 7 l9f

Rickettsia, T2

RlD.4

(regulatory

inactivation

DnaA),

382

Rifampcin,

blockage of transcription

by bacterial RNA

polymerase,

266

plasmids,

402

RISC

(RNA-induced

silencing

complexl, 3M

RNA

base

paring,

duplex formation

and,

l2-l),

llf

catalytic activity See a/so Ribozymes

guanosine-binding

site and, 7 l1-7 lj, 7 llf-7 l3f

RNAase P and, 7I8

substrate-binding site and, 7 I I-7 I 3, 7 | |

f-7

llf

conformational change, with substrate binding, 712,

7 r2f

definition of,

double-stranded, degradation of mRNA, 143-345,

144f,74rf

l' end

generation,

694, 694f,70O

functions of, 128, I28f

G-C

rich region, 694

guide,

7 22-7 24, 7 2)f, 7 24f

hairpin structure, attenuation, ))), J))f

I, replication

of ColEI,

422424,

422f, 423f

L-tg,7t2,712f

mutations,

plasmid

incompatibility

and,

42)424,421f

nucleotide sequences

exons, 38, 38/

introns, 18, 38/

processlng

CTD

in,624-625,625f

early heavy chain expression and, 586-587,

587f

protein

synthesis, 128-129, l28f

reassociation, kinetic

analysis of, 92-9), 92f

replication, central dogma and, tO-l

l, I l/

retroviral,

554, 554f

reverse

transcription, l0-12, I l/

55, t75, t79,698

5.85, I75

455,698

satellite. See Virusoids

sequence changes, 105

7SL,564-565

small

nucleolar,

699-700, 699f

spliced leader, in t/afls-spicing

reaction,

689-690,689f

structure, at attenuator, ))7,

337f

sugar in, 6

synthesis, 258. See also Tlanscription

RNA

polymerases

and, l0

in transcription brbble, 259-260,

259f, 26Of

transcribed

from

pseudogene,

109

translation,

central dogma and, l0-I l, I

types of. Sed Messenger RNA; Ribosomal

RNA;

Tfansfer RNA

U run, 694

in viral

capsid,

731-7)2,7j2f

viroid, l9-2O,20f

in viruses,

RNAase E, degradation of

bacteria mRNA, 141, 14lf

RNAase

(ribonuclease

P), 707,718

RNAases

(ribonucleases),

RNA-coding

genes,

in mitochondria,

70,70f

RNA

editing

definition

oI,

707

guide

RNA and, 722-724,

72)f,724f

individual

bases, 7 2O-7 21, 7 20f,

7 2lf

in trlpanosome mitochondria,

7 2l-7 22, 7

22f

RNAi.

See RNA interferenc€

RNA-inducing

silencing complex

(RISC),

824

RNA interference

(RNAi)

definition

of, 143

generadon

of siRNA,

344, 344f

RNA

silencing and, 345

systematic analysis

gene

expression,

344

RNA ligase, 690, 7 13,

7l3f

RNA

polymerase

activation of repair,

625-627, 626f

active site, 263-264,

264f

886 Index

antitermination

protein

and, 29I-292,

29lf

arrested, restarting

269

-27

attenuation,

337, ))7f

Bacillus subtilis,282

bacterial

coding strands, 266, 266f

structure of

262-26), 262f

subunits, 265-266, 266f

template slfiands, 266, 266f

binding, 323

to ancillary factors,

292-294, 293f,

294f

DNA. 270, 27Of, 275-277,

275f,276f

PRE

promoter,

)68, )68f

wirh

promoter,

repressor-operator

binding and,

3r6

bond breaking

and making, 264,264f

classes,

conf ormation, 264-265, 265

contact,

on one face of DNA, 275-277,

275f, 276f

corc enzyme,267

degradation deficiency,

62 7

DNA binding, 27O,270f

DNA binding contact

points,

275-277,

27 5f, 276f

DNA transcription, in vitro,

81,0

eukaryotic. subunits, 612-613,

6llf

function, 10, 258

genes,

J25, )25f

helix-2 interaction, ) 65

-3

66, ) 66f

holoenzyme

complex, 648, 648f

I,6tl

bipartite

promoter,

614-615,

6lrf

promoters,

transacription termination,

694-695,

694f

il,6rt,64)

indirect

trigger for termination,

cleavage

as,695

initiation complex assembly,

621

methylation at

promoters,

612

promoters,

61,1,8O2

resilience to rearrangement,

647

startpoint, 618-619, 619f

transcription,

624

vllrd

transcription, 781

III, 6T I

downstream and upstream

promoters

for,

6t5-6r6,6t6f

transacription termination,

694-695, 69 4f

rirrrino iniiirri^n

abortive initiation, 268,

268f

open complex, 268,268f

phases,274-275,275f

sigma factor release, 268-269,

268f

size change, 268-269, 269f

ternary complex, 268, 268f

tight binding, 268

initiation of transcription,

loose

binding site, 267

method for seeking

binding sites, 27 0-27 l, 27 \f

nucleosome displacement during

transcription.

779-78t,780f

positioning

factors,

-620,

620f

promoter

binding

rate

ol, 270-27 l. 270f

promoter

recognition, consensus

sequences and,

272-274,274f

reading into

origin,

449450

replication at 5'end and,

)94, )94f

sigma factor. 154

control of

DNA

binding, 27 l-272, 272f

rcIease,

268-269, 268f

specificity

control and, 267, 267f

substition,

promoter

recognition

and,

278,278f

size, vs nucleosome

size,78,779f

specificity, control

of,

267,267f

sporulating cells, 284

stalled, MFD

protein

and, 625-626, 626f

structure, 262-265, 262f-265f,

)37

)J7

with TFIB, 622-623,

62)f

phage,

261-262,262f

phage,26I-262,262f

transcription,

642, 64)f

bubble formation, 259-260, 259f,

26of

catalysis, 260-261, 26If

of delayed early

genes,292

immediate

early

genes,

292

of lambda

gene,

292-29),

293f

transcription

units and, 292

yeasI,26),263f

RNA regulator, control,

plasmid

ColE I compatibility

system, 422-424, 422f, 42)f

RNA silencing, RNA interference and, )45

RNA

splicing

complex formation, 677-679,679f

alternative

reactions in, 46-47, 46f, 47f

splice

junction

differential use,

685-688,

686f,687f

apparatus, 674-675

Bl complex formation,

679,679f

82 complex formation, 67 9f

Cl complex formation, 679f

C2 complex formation, 679f

dJ-splicing

reactions, 688, 688/

control,

670

definition

of, 34,34f,38, 669

E complex conversion to A complex,

677-679

complex formaion, 677, 678f,

679f

exon

definition

process,

67 8-679,

67 8f

intron definition

Vocess,

67 8-67 9, 67

exon

junction

complex, 682, 682f

initiation, by Ul snRNA, 676-678,677f,678f

as intermolecular reaction, 688

junctions,

67 l-67), 672f

lariat {ormation, 680, 68)-684, 684f

location,

670,67Of

mRNA

export and,, 682-683, 682f,68)f

nuclear, vs

group

II, 685,685f

pathway,

672,672f

pre-mRNA

lariat formation,

673-674,

67)f

sIages,67)-674,67)f

sites, 670-67

SnRNAS

pairing

reactions, 680-681, 680f,

68lf

spliceosome

form

aion, 67

4-67 6, 67 5f

spliceosome See Spliceosome

-..ll^:..^ ^--^-^+,,-

JP'rUrrE dupordrur

alternative,

681-682

snRNA components, 680

stages, 676

systems, types ol, 670

tissue specificity, absence of, 672

transesterilication, 67

trans-splicing reactions,

688-690,

688/

tRNA

cleavage stage, 692, 692f

endonuclease, 69

I-692, 69 lf, 692f

evolution of, 691-692, 69lf

ligation stage, 692, 692f

unfolded

protein

response and, 69),

693f

yeast,

690, 690f,69lf

U6-U4

pairing,

680, 680f

RNA splicing and

processing,

669-7Ol

RNA

viruses,

recombination,

459

RodA,4I2

Rolling circles

generation

of single-stranded multimers, 387,

396-)97, 796f

of T-DNA,

405406, 405f

products,

387f,

)96-)97, )96f

replication

phage

genomes,

)87f, 397-798

viroids

and, 7 l8-7 19

virusoids and, 7 l8-7 19

Rom

protein,

421

Rotational

positioning,

of DNA on

nucleosome,

777

777f

rpos

gene,342

r-proteins,

RRF

(ribosomal

recycling factor),

174, 175f

IRNA See Ribosomal RNA

RseA

protein,

factor and, 279,279f

segments,

554, 554f

R-UR 554

rut sile,288-289,289f

RuvA,47)474

RuvAB

complex, 47347

4, 47 4f

RtrvB,473474

Ruv system, Holliday

junction

resolution,

472473,473f

RXR

receptor

(9-crs-retinoic acid receptor),

657-658,657f

RyhB, 341

S archar omyces cer

evisiae

chromatin

remodeling complexes,

800, 800/

DNA

centromeric,

746

short

conserved sequences

in, 7 47

7 47f

genes

cse4,824

exons,43,44f

expressed,

measurement

of, 94, 94l

repair,5l5

surveillance systems,

I 44- I 45

genome,

79-80,79f

mitochondrial, 69

nucleosome

positioning,

777

size,

family size and, 8I,

snoRNAs,

699

mating type,

488489, 489f

meiosis,

timing of events

in, 468, 468f

mitochondria

DNA,

70-7r, 7u

genome,

MSA repair system,

509

musSl mutanat'474

replication origins,

isolation of, 784-)85,

)85f

RNA

polymerase

II, 612, 6l3f

RNA splicing, 677

IRNA splicing,

690, 690f,691f

SAGA, 807

SAGE

(serial

analysis

gene

expression),

sarellire DNA

anthropod,

short identical

repeats, I l9-120,

I l9l

definition

of, 100

density

gradient,

I 18,

18/

heterochromatin

and,

I l7-I I9, 118f,

1l9f

mammalian, hierchical

repeats,

120-12), 12lf-lzjf

in mouse

centromeres,

119, ll9f

sequencing,

I20

Satellite

RNAS See

virusoids

Satellite

tobacco

necrosis virus

(STNV),

chizo s ach aromy ce s

omb e

cir

genes,

S\2

Index 887

DNA, centromeric. 746

genomes,

79-80.79f

SCID

mutation

(severe

combined

immunodefiicency

mutation),

586

Scrapie, 20, 819

scRNAs

(small

cytoplasmic RNAs),

675

Scyrps, 675

SecA,247-249, 248f

SecB, 247-248,

248f

Sec61 complex,2)2

Secondary attachment

sites. 483

Secondary immune response.

575,

594

Second-site

reversion,

of mutation,

Sec system, 247-249,

247

248f

Sector,5lS-519

Sec6

translocons, 2))-234, 234f,

239

SecY complex, 232

SEDS family, 412,414

Segmental duplications,

in human

genome,

85-86,85f

Segregation

chromosomal,

panitioning

process

and, 417-419,

418f

mitochondrial,

424425,

424f

Seleno-cys-tRNA. 199, l99f

Self-assembly, oI

protein,

22),

224

Self-cleavage, of viroids and

virusoids, 719,7

l9f

Selfish DNA,

Self

-splicing

(autosplicing)

group

I introns,

transesterification

in, 707-709,

708f-7

rof

intermolecular

reaction,

709

primary

cycliTalion. 708. 7l0f

reverse cyclization,

708, 7 l0f

Semiconservative replicarion,

of DNA. 8-9, 9/

Semidiscontinuous replicarion,

4)44)5,

4)5

Sense

strand

(coding

strand),

129, l29f

Septal ring, 4I4

Septum

formation

(septarion)

bacterial, FtsZ

and. 4l)414,4t4f

in bacterial daughter

cell division,

411412,

41lf,4r2f

FtsZ

and, 4l?414,414f

location, min

gene

and, 415,415f

pedseptal

annulus

and, 4114I2,

41Lf

Serial analysis

gene

expression (SAGE),

Severe combined immunodefiicency

(SCID)

mutation,

586

Sex steroid hormones,

as activators,

654l

SFI splicing factor,

677

SF2 splicing {actor,

686

SGA

(synthetic

genetic

array analysj,sl,

91, 91f

Shine-Dalgarno

sequence. 161-162,

l6If,

t80, )24

Short interspersed repeated

segments

(SINES),

56)-564,564f

Short

patch

pathway,

for

excision repair

mammalian

cells, 505,

505/

Short sequence

eLemenrs.

activator

binding.

627-628,627f

Sigma factors

Bacillus subtilis.282

cascades,

282-28)

configuration,

at open complex

formation,

280,28rf

control

of DNA

binding. 27 l-27

2, 27 2l

of sporulation,

28)-286,

284f-286f

core enzyme, 28O,282f

DNA contact, 280-282,

281f,

282f

Escherichia

rcli, 27 8-280,

279f

lytic

cascade and,

354

phage

developmeil

and, 282-28j,

283

promoter

recognition, consensus

sequences

and,

279-280,280f

recognition of heat shock

gene promoters,

650

rercase,

of RNA

polymerase,

267,

267f

st4, 281-282

factor, 279,279f

s7o factor, 278, 280-281, 28lf

sF factor, 284-285, 285f

sG factor. 284-285, 285f

structure

conserved regions, 280, 280/

helix motif, 280-281

281[

substition,

promoter

recognition and, 278, 27 8f

Signal ends, 582,582f

Signal

peptidase,

229

Signal recognition

particle (SRP)

Alu domain. 2)0,2)0f

bacterial counterpart, 2)0-2i I

binding with signal sequence. 228-229,229f

components, 564-565

conformation, signal

binding and,

230, 230f

functions,

228,2)0

S domain,

2)0,2)0f

SRP receptor interaclion, 2)0-231, 23lf

structure, 229-210, 230f

Signal recognition

particle

receptor

(SRP

receptor), 230

Signals, for

protein

synthesis, in free ribosomes,

222,222f

Signal sequences

anchor

sequences as, 2)7

of bovine

growth

hormone

228, 228f

for

protein

translocation initiation, 227-228,

227f,228f

interaction with

SRP,

228-229,

229f

Silencers, repression of silent

cassettes

492493, 493f

Silencing

definition of, 802-801

telomeric,

821

Silent

cassettes

aI HML locus, repression

oI, 49249), 49)f

at HMR locus, repression

of., 492493, 49)f

for

yeast

mating,

488489, 489f

Silent mutations, 27

Silent sites

definition

of,

10,1-105

divergence of. |

05-l 06. I 05/

mutations in, I05

Simple sequence DNA

(sarellire

DNA). I l7

SINES

(short

interspersed repeated

segments),

56)-564,564f

S1N

gene,

495

Single copy replication

control, 177

Single

nucleotide polymorphism (SNP)

definition

of, 57

frequency

per genome,

57-58,

for

genetic

mapping,

58-60

Single-strand binding

prorein (sSB),

436-418,

4)6f,438f

Single-strand exchange,

5 i0-5 1 l, 5 10/

Single-strand invasion,

464

Single-strand

passage

reaction, 480

Single-strand uptake

(single-strand

assimiliarion)

catalyzed by strand-transfer

proteins.

47t47),472f

definition

o{, 47 I

Single X

hypothesis, 827,

827f

siRNA

(short

interfering

RNA). )43, )44,

j44f

sIR

proreins.

492,49),

49)f

S[]/Sir4,823

Site-specific recombination, chromosome

segregation

and, 415417,41.6f

Slippery sequences, frameshift mutations and,

2rj-2r4,2t3f

Slow-stop

mutants, 4294)0

SL RNA (spliced leader RNA). rrars-rpicing reaction.

689-690,689f

Small

cytoplasmic RNAs

(scRNAs),

675

Small nuclear RNAs

(snRNAs)

definition of, 675

functions, 684

generation

of l'end of histone nRNA,697,697f

in RNA

splicing

pairing

reactions, 680-681,

680f, 681f

spliceosome f ormatio\, 67 4-67

6, 67 5f

base-paired structure, 67 5-67 6,

67 6f

initiation of splicing, 676-678, 677f,678f

mutations,

676-677, 677f

Small

nucleolar RNAS

(snoRNAS),

699-7OO, 699f

SMC

proteins

(structural

maintenance

chromosome), 828,829f

proteins,

676

SMRT corepressoa 658,

6581 808

SNP see Single

nucleotide

polymorphism

snRNAs Sae Small

nuclear

RNAs

snRPs, 680

Snurps,675

Solo ds, 559-560

Somatic mutations

immune diversity and, 590-591, 591f

induced,

by cytidine deaminase and uracil

glycosylase.

591

-59

), 5921

UNGand,590

Somatic recombination

allelic exclusion and, 581

of immunoglobulirs, 57 6-57 7

Somatic

segregation, 67

SOS box, 514

SOS response, 5ll

Spacers,6I5

Sparsomycin,

inhibition

peptidyl

transferase,

I 78

Species differences

exons and, 42-4), 4)f

gene

number, 78, 78l

gene

organizatron,

5l-52, 52f

genome

sequences, 66-67,

67f

genome

size, 60-61, 60f, 6lf,78,78f

globin gene

clusters, 1 1 l-1 I 2

introns, 4l

proteins,

104

phase,

383, 49J,774

Spliced leader RNA(SL RNA), /rdnr-spicing

reaction,

689-690,689f

Splice

junctions,

in alternative RNA

splicing, 685-688,

686f,687f

Spliceosome

components,68l

oennrnon ot,6/t,6/)J

formation,

5 snRNPs and, 679-681,

679f- 68lf

REF

proteins

binding

to splicing

junctions

and,

682-68),683f

U I 2

-type,

681-682

Splice recombinant

DNA, 461

Splic€ sites

)" 672

cvtting, 67jf,674

recogntllon

oI/ 6

/+b /

5" 672

binding to Ul snRNP. 674

cutlrng, 673-674,673f

888 Index

mutations,

676-677,

677f

recognition

of, 67 4-67

branch, recognition

of, 674-675

crypl\c, 67 4

definition oI, 67 0-67 l,

67 lf

generic,672

recognition,

673

Spm element,

gene

expression

and,, 542-544,

543f

SpoIIIE

protein,

419

Spontaneous mutarions

definition of, 14

horspors,

t7-).9, t8f, 19f

frommodifiedbases,

l8-19, I8l

l9l

SpoI 1

protein, generation

oi double-strand

breaks,

467468,467f

Spore formation, in Ascomycete

tetads, 47

5, 47 5f

Sporulation

cascade, 28)-284, 284f

control, by sigma factors, 283-286,284f-286f

forespore,

284-286, 284f-286f

mother

cell,

284-286,

284f-286f

Sporulation

genes,

841 9

sr2

protein,

278

SRB loci,

648

SRE

(serum

response

element), 649

S regions, 588, 588,

600

sRNAS

E coli,34l-)42,342f

SRP See Signal recognition

particle

SRP

receptor

(signal

recognition

particle

receptor

230

proteins,

677

SSB

(single-strand

binding

protein]l,

436-4)7

4364)8,

436f, 4)8f

Startpoint,258

STE

genes,

488

Stem-loop binding

prorein

(SLBP),

697

Steroid receptors

activation, by ligand binding,

656, 656f

as activators, 65)-654, 654f

definition

of, 65 I

DNA

binding as dimers, 655

recognirion

response

elements, by combinatorial

code, 657-658, 657f,

658f

SMRT corepressor binding, 658,

658f

zinc fingers,

65r-656, 655f,656f

Steroid response elements, half

sites, 657, 657f

Stop codons

definition of, 172, 197, l97f

f r:mechifrino :r ) I d

novel amino acid insertion in, 199,

l99f

Stop-transfer signal, 216-2)7

2j7f

Strand

displacement, )94, )95f

Strand-exchange reactions, f

or replication repail

512-51),5r2f,5r)f

Strand-transfer

proteins,

catalysis, of

single-strand

assimiliation, 47 147

47 2f,

47 3f

Streptomycin inhibition, o{

protein

synthesis, 2I0-2Il

Structural maintenance of chromosome

proteions

(sMC proteins),

828, 829f

Substitutions, during DNA replication,

412

Subviral

pathogens,

su(HW)

gene,

84-7 85, 7 85f

Suicide substrates, 484, 485

Supercoiling, DNA

in bacterial

genome,

7 35-7 36, 7

3rf,

)6f

DNA

structure and, 476478, 476f, 477f

gyrase

and, 481482, 482f

introduction by topoisomerases,

47 8479, 479f

inverted, release of, 482,482f

negaIive,477

in nucleosome,

7 66-7 67

7 66f

phage genome

replication and, 198

positive,

477

structure

and, 476478, 476f,477f

torsional

tension, 716

in transcription, 27

-27

8, 27

Superfamily, 51, 574

Suppression

definition

of, l7

nonsense, readthrough

and,

208-209, 2O8f

Suppressor

definition of, I 7

frameshift,

)1, 2).)-214, 2llf

IRNAS, 206-207, 206f

competition with

wild-type

IRNA, 208-209,

208/

missense, 206-207, 2O7f

mutations, 209

nonsense,

20 6-208, 20 6f, 207

sup35

proreins,

816-8)8, 8)7f

Su(HW)

proteins,

784-785,

785f

Su(var)

proteins,

Sl2

Surrogate light chain

(SL

chain), 595

Surveillance

systems, 144-145, l45f

)ulvlvaf, telomeres

ano,

/>2-/>J. /121, /)tJ

suvl9Hl, 808,822,822f

SV4O DNA, 77I

Sv40 enhancer, 6)0, 63Of

SV40 minichromosomes

DNA

supercoiling, 7 66-7 667

766f

nucfeosome

gap.

/66-/6/, /6/l

transcription

complexes, 77 8, 77 8f

SWI

gene,495

SWI/SNF complex

binding, 810, 810/

definition of, 799-800,

800/

recruitment, 801

Swi5 transcription factor, 80 I

SWl5 regulator,496

SxI

protein,

686

Synapsis

(chromosome

pairingl,

46 |

Synaptonemal complex

axial

element formation, double-strand

breaks

and,

468,468f

connection,

with

recombining chromosomes,

465467,

466f

definition

of,

46 I

formation, 465466

aiter double-strand breaks,

467469, 468f

independent

from chromosome

parrng, 469

recombination

and, 467

468

mutations,

466467

structure

axial elements, 466

central elements, 466, 466f

jaleral

elements, 466,

4661

nodes or recombination nodules, 466,466f

proteins

in, 466467, 466f

Synonyms,190

Synteny,

66-67, 67f

Synthetic

genetic

array analysis

(SGA),

91, 9ll

Synthetic

lethal, 9

TAF',619, 621

"Take-off"

sites, in bypassing, 214-2I5,

214f

Tandem

gene

clusters, restriction

map, I l2-l

I I 3/

Tandem repetition, I l7-l l8

T antigen, 45 1

TAP/MEX transport

protein,

68), 68)f

rar-binding

sequence, 644,

644f

TATA-binding

prorein (TBP),

615,619-621,

620f,

62lf

TATA box, 619, 621, 621f,623, 628, 628f

TATA element, 618

TATA-less

promoters,

6I9

tat

protein,

644, 644f

TBP

(TATA-binding prorein),

615, 619-621, 62Of, 62lf

cell

receptor

(TCR)

ab, 57 6, 595-596, 596f, 598

antibodies on, 598

cD3

proteins

and, 598-599, 599f

definition of, 57),574

development, 598,598f

gd.,

576, 595-596,596f

gene,

organizatio\

oI, 596-597

596f, 597f

MCH

protein

and, 597-599,

598f, 599f

proteins,

596

T cells

lymphocytes)

clonal expansion,

574-575, 574f

cyloloxic,57l

definition

of, 572

development, 598,598f

helper,572

killer

cytotoxic, 571

TCR SeeTcellreceptor

T.DNA

Acrobacterium tumefaciens,

402406, 4OJf4O5f

genes,

crown

gall

disease

and, 402405, 40)f, 404[

ldansfer,

405406,

405f

Telomerase, in telomere

synthesis, 7 50-7 52,

5 ll

Telomere

chromosome

end sealing,

749-750, 749f,750f

definition of,

748

extension

by recombination,

7 52-7 5j, 7 52f

{unctions,750

s_trortenrng, / >2-

/ )

/ J2J

simple repeating sequences,

748-749, 7 49f

survival and,

52-7

53, 7 52f, 7 53f

synthesis, by

ribonucleoprotein enzyme.

750-752,75tf

Telome ric silencing, 821

Temperature, environmental,

heat-related

genes

and,

278-279

Template recognition, in transcriptio\,

260, 26lf

Template strands

8-9,

9f, 258, 258f

T4 endonuclease

(Ta-pdg),

506

Teratomas, 402

Terminal

proteins,

viral

initiation and, 394-39r, 395f

Terminal uridyltransfetase

(TUTase),

723-724, 724f

Terminase, 7 )2-7 )),

33f

Termination

of DNA replication,

429

mode of elongation

and, 295

pausing

and,

288

prevention, by

pQ,

294-295

protein

synthesis,

I 55, I 55/

RNA

polymerase and, 29j-29 5,

of transcription,

26I,

26lf

rho factor and,

287

288-291,

Termination codons

alterations,

sporadic,

197

-198,

definition

of, 12

2e4f

289f,29Of

re7f, resf

nonsense supressor

tRNA,

207

-2O8,

2O7f

for

protein

synthes$,

172

recognilion by

protein

lactors.

lTr-174,173f. 174f

Terminators

bacterial,

286-287,

287f

inE coli,287-288,287f

inrrinsic,

287-288, 287

rho-dependent,

287, 288

delinition

of, 258,

258f

rho-dependent,

29O,

290f

Index 889

Tetrad. ascomycete, 47

5, 47 5f

Te tr a hymen a t lt e r mop h i I a

genetic

code

changes, I 97

group

I intron

inE coli,TlO-7ll,7llf

secondary structu re, 7

09-7 10, 7 l0f

self

-splicing.

7 07

-7

09, 7 0

8f-7 l]f

histone modification,

804

nrSlone

lrSage. / /+

TFs See Transcription

tactors

Thalassemias, de lctions in,

I l0-l I l, I I I/

Thermts aquaticls.

signra lactor,

280,280f

Thermus the nno

hl1ri.r, ribosome,

strucrural

conlormarion, l8l

Third-base

degeneracy, l9l, 192, l92f

Thymidine dimers,

excision repair

system, 516,516f

Thymine,6, l8-19, l8f

Thyroid hormones,

as activators,

654f

TIM complexes, mitochondrial,

24', 244,

244f

plasmids

definition of, 406

crown

gall

disease and, 401-402,

402f

T-DNA. 402-405, 40)f,

4O4f

71a loci

proteins,

600

TLF,620

T4 ligases, 444

TLRS

(toll-like

receptors),

602-604,

6olf

T lymphocytes Sse T

cells

TnA family. replicarive

transposition,

r4-r6, 535f

tnpA

gene,5)5,535f

tnpR

Eene,

5)5, 5)5f

Tnl0

transposition, nonreplicative

mechanism,

518

tranqp')\('n. nurrrcplicat

e tranrposition,

5)4,5)4f

Tn10 transposon,

ISI0R

acrive module,

promotors

in,

5)6-5)7, 5J7f

Tn 1 0 transposon, nonreplicative

transposition,

53)-5)4, 5))f

Tn10 transposon,

transposirion,

SS6-5J8, 537f

tn transposons or composlte

transposons,

525-526,

525f,526f

lolerance, ) /J

Toll-like receptors

(TLRS),

602-604, 60jf

TOM complex, mitochondrial,

24)-244, 24)f

topA

gene

mutations, 4l8

Topoisomerases

activiry, similarity wirh

sire-speciific

recombination,

484486,485f

introduction

ol supercoiling.

47 8-479,

479f

type 1, 277

479

single-strand DNA

and, 479, 480,

48Of

type

ll,

479 See also

Gyrase

double-strand DNA

and, 479, 481,

48If

Topological isomers,

477

TPA response

element

(TRE).

650

phage

RNA

polymerases,

26l-262,

262f

phage

RNA

polymerases,

26I-262,262f

tra

gene,

686

Trarler, )), )4f

TraM,

400

TRAM

(translocating

chain-associated

membrane),

23),233f,239

Traur-acting DNA

sequences, 302,

)O), JO3f

?anj-acting

mutations,

16, l6l

Tranr-acting

sites,

j5-)6.

36f

Transcribed

genes,

nucleosomes

and, 777-778,

778f

Transcript. l8

Transcription.

256-29

activation,

640-665

by CRP activatot

l2l

DNA binding

and, 644

independence from DNA-binding domain.

64)-645.644f

basal level, 106

base

pairing,

"transcription

btbble," 259-260,

259f,260f

coding strand, 258, 258f

constiutive, 109

control

by antitermination, 291, 29lf

enhancers, 6l l-612, 612f

promoters.

6Il,6l2f

by translation. ))6, ))6f

definition of, ll2

DNA sequence, 258

gene

expression, ))-34, )4f,258-259

histone

octamer displacement, 779-781,

779f, 780f

initiation, 260-261, 261f,

610

eukaryotic

gene

expression and, 641-642,642f

RNA

polymerase

and, 267-269, 268f

transcription factors

and, 621-622

model systems, 261-262, 262f

nRNA. 129, 129f,156, l56f

nucleosomes

and. 777

-77

9, 77 8f, 779f

products. primary

transcript, 258

promoter

recognition, consensus sequences and,

272-274,274f

promoters,

258,258f

rDNA cluster, II), ll4f

repair and, 625-627,

626f

repair systems in

yeast

and, 5

repression, by histone deacetylarion,

808, 808/

restarting,

arrested RNA

polymerase

and, 269-270

sldges, 260-261, 26lf

elongation, 26I,26lf

initiation,

260-261, 26lf

template recognition,

260, 26lf

startpoint, basal apparatus and, 642

supercoiling,

27 7

-27

8, 27 7

template strand, 258, 258f

telmtnatron

attenuation

hairpin

structure in RNA,

3)), )))f

bacteria RNA

polymerase,

286-287, 287

rho factor

and, 287, 288-291, 289f, 290f

by RNA

polymerase

694-695, 694f

by RNA

polymerase

lII, 694-695, 694f

translational contol

of, ))5,3)5f

terminators, 258,258f

twin domain model. 277. 2771

Transcription factors

(TFs)

definition

of, l0l

'IF1r4,622

TFtrB,

with RNA

polymerase,

622-621, 621f

TF1D,

6t9-620, 62t.798

activator contact,

647, 647f

binding

TATA

box. 622

TFTE,624

TFff,62)

TFIH,

624, 625-626,

626f

TFil,624

TFtilA,

617, 798

TFDrB,6t6-6t8,6t7f

types,

642-64), 64)f

Transcription

units. 258,

292

Transcriptome,

Transducing viruses,

558-559, 558/

Transesterilication

group

intron self-splicing, 7O7

-7

09,

708f-7

Ilf

protein

splicing, 7 24-725. 725[

in riboTyme catalytic reaclions.

7 1

7 |

in RNA

splicing, 674,

674f

in splicing reactions, 68), 684f

Transfection,5

Transfection

systems,

promoter

characterization,

6 I

Transfer

genes,

plasmid,

398-799, )99f

Transfer region, 399

Transferrin nRNA, iron-responsive element,

142-14),

r42f

Transfer RNA

(IRNA)

,ltern:tivP oenPs 49

anticodon, specilicity determination and, I I l, 1 lU

base modifications, 194-196, l95f

anticodon-codon

pairing

and, I96-197, 196f

bases

invariant

or conserved,

I I

semi-invariant or semi-conserved,

I J

hinrJino <ires 169 17Of

A,154,

r54f, r60,177,

t78f

E, r54, r54f, 178f

P, 154, 154f, 160, 177, 178f

charged See Aminoacyl-IRNA

charging

process.

1)1, 20O-2O1, 2O0f, 209

cognate,

200

kinetic

proof

reading and, 2Q3-20

4, 20 4f

conformational structure, active sires and, 205-206,

205f

contact, with

2lS rRNA, 182

deacylated,

delinition of, 14

3' end,194,

l94f

5' end,194, l94f

E site, 182

function

of,

128-129

identification, by synthetases, 201

interactions

with ribosome, 154-155,154f, l55f

with IRNA, 180

isoaccepting, 200-20l

modified bases, l9,t-197, ).95f, 1.96f

mutations

missense, 206-207, 2O7f

nonsense, 206-207, 206f

nomenclature, I I I

numbering

system, 111

A site.

protected

regions, 181

size of,

l28f

specificity, IlI, llU

50S

subunit,

182

structure, 128-129, 128f, 177-178,

178f

acceptor arm, 130-111, l)Of, lj2f

anticodon arm,130f, l)1, l)2f

arms,

ll0, 130f,132f

base

pairing,

130f, I)l

D arm, I 10, l)1, IJ2f

enzyme-related

changes, 202, 2O2l

extra arm, llof, l3l

loops,130,

110/

secondary or cloverleaf, 130-131,

130/

srems.

10.

Jjl. lJ2. l32f

tertiary L-shaped, 13I-l)2, l32f

TyC

arm,

130f,

l)1, l32f

suppressor

competition with wild-type tRNA,

208-209,208f

nonsense

codon recognition, 206-207,

2O6f

synthesis. from longer

precursors,

194, 194/

wild-type, competition with

suppressor IRNA,

208-209,208f

Ttansformation, 3-4

transformer

(tru) gene,

686

890 Index