Cel

lBi
ologyLec
tur
eNot
es

I
ntr
oduc
tion:

A.Def
ini
tionofac
ell
:fund
ament
als
truc
tur
alandf
unc
tionaluni
tofal
lli
vingor
gani
sms

B.Char
act
eri
sti
csofc
ell
s:

1)Cont
ainhi
ghl
yor
gani
zedmol
ecul
arandb
ioc
hemi
cal
sys
temsandar
eus
edt
ost
orei
nfor
mat
ion

2)Us
eener
gy

3)Cap
abl
eofmov
ement

4)Sens
eenv
ironment
alc
hanges

5)Cand
upl
ic
ate(
trans
fergenet
ici
nfor
mat
iont
oof
fsp
ring)

6)Cap
abl
eofs
elf
-regul
ati
on

-Mos
tcel
lsar
emi
cros
cop
ic(
inv
isi
blet
othenakedey
e)andt
hus
,ami
cros
cop
eisneed
edt
ovi
ewmos
tcel
ls
.

C)Hi
stor
y:

-Di
scov
eryoft
hec
ellf
oll
owedb
ythed
evel
opmentoft
hemi
cros
cop
e

A. 1665-RobertHooke-obs
ervedcel
lsf
r omthefrui
tingb
odiesoffungi
B. AntonvanLeewenhoek-observ
edav ari
etyofcel
lsandcall
edthem"animal
cul
es"
C. 1830’
s-TheodorSchwannandMatthi
asSchlei
dendevel
opedthecel
ltheory

-Cel
lTheor
yst
ates
:

1. Al
lli
vingorganismsarecomposedofcell
s
2. Cel
lsarethef uncti
onaluni
tsofli
vingorgani
sms
3. Cel
lsaris
ef romp r
eexist
ingcel
lsvi
ad i
vis
ion

D)Loui
sPasteur-d
evel
opedt
het
heor
yofs
pont
aneousgener
ati
ont
hati
sthatc
ell
scoul
ddev
elopf
rom
non-l
ivi
ngmatter

-Al
sowor
kedonp
rob
lemas
soc
iat
edwi
tht
hef
erment
ati
onofFr
enc
hwi
ne

-1857-dev
elopedapart
ials
ter
il
izati
onproces
scall
edp as
teuri
zati
on-inv
olv
esheat
ingat
amod er
atet emper
aturest
oreducethenumberofli
vingmicr
oorgani
sms

E)1865-Mend
el-d
emons
trat
edt
hatc
ell
ulart
rai
ts(
phenot
ypes
)wer
einher
ited

-Seeds
hap
eandc
olori
ngar
denp
eas

-Named"
Fat
herofGenet
ics
"

F)1871-JohanFrei
dri
ckMi
esc
her
-is
olat
ednuc
lei
cac
idsf
romc
ell
s"nuc
lei
n"
G)1889-R.
Alt
man-p
uri
fi
ednuc
lei
cac
ids

H)1944-Os
wal
dAv
ery
,Col
inMac
Leod
,andMac
LynMc
Car
ty-

-Demons
trat
edt
hatDNAwast
heher
edi
tymol
ecul
e

-DNAc
oul
dtr
ans
for
mbac
ter
ialc
ell
s

I
)1952-Al
fredHer
sheyandMar
thaChas
e-al
sod
emons
trat
edt
hatDNAwast
heher
edi
tymol
ecul
e

-Rad
ioac
tiv
eDNAf
romav
iruswasab
let
oinf
ectandt
rans
for
mbac
ter
ialc
ell
s

J)1953-JamesWat
sonandFr
anc
isCr
ick-d
evel
opedt
he3-Ds
truc
tur
eofDNA

K)1958-MattewMesel
sonandFr
ankSt
ahl
-demons
trat
edt
hatDNAr
epl
ic
atedb
yas
emic
ons
erv
ati
ve
met
hod

L)1961-Br
enner
,Jac
ob,Mes
els
on-d
isc
over
edRNA

M)1966-Ni
renb
ergandKhor
ana-el
uci
dat
edt
hec
hemi
calnat
ureoft
hegenet
icc
ode

N)1972-1973-Ber
g,Boy
er,andCohen-d
isc
over
edgenec
loni
ng

O)1975-Gi
lber
tandSanger
-dev
elop
edc
hemi
calt
echni
quest
orap
idl
ysequenc
eDNA

 
Cel
lSt
ruc
tur
e:

I. Mostc ell
saremicr
oscopi
candc annotbeseenbythenakedeye.
II. Mic
r oscopesweredev
elopedtov i
sual
izec
ells
.
I
II. Resolutionist
heminimumd i
stancewhere2ob j
ectsc
anb evi
sual
lys
epar
ated

-Unr
esol
ved

-Par
tial
lyr
esol
ved

-Res
olv
ed

-Dep
end
son:

a. Wavelengthofli
ght
b. Ref
r acti
veindexofthemed
ium
c. Ofthelight

-Thenakedey
ecanr
esol
vet
wos
epar
ateob
jec
tss
epar
atedb
y200um

Met
rics
yst
em:

-1met
er=3. 3f ,1km=103m,1c
eet m=10-2m,1mm=10-3m,1um=10-6m,1nm=10-9m,1A=10-10m,
-12
1pm=10 m
I
V.Li
ghtmi
cros
cop
e:

-Canr
esol
vet
woob
jec
ts100-200nmap
art(
inc
lud
ingc
ell
sandl
arges
ubc
ell
ularor
ganel
les
)

-Us
esd
iff
erentl
ights
our
cesandp
att
ernsofi
magef
ormat
ion

a. Bri
ghtfiel
dd)dif
ferenti
ali
nterf
erence
b. Darkfi
elde)fl
uores
c enc
ec)phasecont
ras
t

V.El
ect
ronMi
cros
cop
e:

-Us
esab
eamofel
ect
r e-)r
ons( athert
hanl
ightasani
ll
umi
nat
ions
our
ce

A.Tr
ans
mis
sionEl
ect
ronMi
cros
cop
e(TEM)

-El
ect
ronsf
ormi
ngt
hei
magef
ocus
edt
hrought
hes
pec
imen

-Shor
twav
el hofe-b
engt eami
mpr
ovest
her
esol
uti
onofTEMt
o5A(
.5nm)

-Canr
esol
ves
mal
lsubc
ell
ularor
ganel
lesandl
argep
rot
eins

B.Sc
anni
ngEl
ect
ronMi
cros
cop
e(SEM)

-Us
edt
oexami
nes
urf
acesofc
ell
sori
sol
atedc
ell
ulars
truc
tur
es

-e-b
eam"
scans
"thes
pec
imen

-Res
olut
ion5t
o10nm

Pr
okar
yot
icCel
ls
-smal
landp
rimi
tiv
ebac
ter
iaandb
lue-gr
eenal
gae(
cyanob
act
eri
a)

Gr
eek:Pr
o=b
efor
ekar
yon=nuc
leus

-Lac
kss
pec
ial
izedi
nter
nalmemb
rane-b
oundc
omp
art
ment
sknownasor
ganel
les

-Cellmembrane-funct
ionsint
ransport,t
hemovementofsubstancesinandoutoft
he
cel
l,andinenergyproduct
ion(
breakdownofl
argemolec
ules,p
hot osynt
hesi
s)

-Cel
lwal
l-gi
vess
truc
tur
als
trengt
h(r
igi
dit
y)t
othec
ell

-Cap
sul
e-j
ell
y-l
ikes
ubs
tanc
ewhi
chp
rot
ect
sthec
ellwal
lfr
omenv
ironment
ald
amage

-Nuc
lei
od-c
ont
ainsas
ingl
eci
rcul
armol
ecul
eofDNA(
stor
esgenet
ici
nfor
mat
ion)

-Cy
top
las
m-r
egi
ons
urr
ound
ingt
henuc
lei
odandwi
thi
nthec
ell
memb
rane

-Cont
ainsr
ibos
omesandRNA(
sit
eofp
rot
eins
ynt
hes
is)

-Vac
uol
e(v
esi
cl
es)
(bl
ue-gr
eenal
gae)
-si
teofp
hot
osy
nthes
is(
stor
age)

-Fl
agel
lum-p
rot
einf
ibert
hef
unc
tionsi
nmov
ement
Eukar
yot
icCel
l-(
eu=t
ruekar
yon=nuc
leus
)

1. Posses
s esacomp l
exmembr
anesys
t em
2. Hasat ruenucleus
3. Dis
tinctmemb r
ane-boundi
ntr
acel
lularc
omp
art
ment
scal
ledor
ganel
les

-Nucl
eus-dark-s
tai
ningb
odywi
thi
nthec
ellb
yenc
los
edani
ntr
acel
lul
armemb
ranec
all
ed
thenucl
earenvel
ope

-Nuc
learenv
elop
econt
ainsp
ores
,whi
char
efi
ll
edwi
thar
ingofp
rot
einsc
all
edannul
us

-Cont
ainsDNAi
nthef
ormofc
hromat
inf
iber
s

-DNAi
sli
near(
li
nearDNA+p
rot
eins=c
hromos
ome)

-Nucl
eol
us-ac
ellor
ganel
lei
nthenuc
leust
hatd
isap
pear
sdur
ingp
artofc
ell
div
isi
on.Cont
ainsr
RNA
genes

-Nuc
leusal
soc
ont
ainsRNA(
mRNA,r
RNA,andt
RNA)

-Tr
ans
cri
pti
on-c
onv
ers
ionofgenet
ici
nfor
mat
ionf
romDNAt
oRNAoc
cur
sint
henuc
leus

-DNAr
epl
ic
ati
on-d
upl
ic
ati
onofgenet
icmat
eri
al

-Cy
top
las
m:maj
orp
ort
ionoft
hep
rot
opl
asmi
csub
stanc
ewi
thi
nthec
ell
memb
rane

a. Ri
bosomes-acyt
opl
asmicp
arti
cl
ethatc
ont
ainsRNAandp
rot
einandi
sinv
olv
edi
nthe
pr
ocessofprot
einsynt
hesi
s

-Tr
ansl
ocati
on-pr
oces
swhi
cht
akesp
lac
eint
hec
ytop
las
mandc
onv
ert
sgenet
ici
nfor
mat
ioni
n
RNAint
op r
otei
ns

-Ri
bos
omescanei
therb
efr
eel
ysus
pend
edi
nthec
ytop
las
morat
tac
hedt
oint
rac
ell
ular
membr
anes

a. Endopl
asmi
cret
iculum(ER)
-anet
wor
kofi
ntr
acel
lul
armemb
raneswher
esec
ret
ing
protei
nsar
esynthesi
zed

-Rough
ER-the
ER+
ri
bosom
es

-
Smooth
ER-the
ER
wit
hout
ri
bosom
es
 -
Functio
nsin
the
breakdo
wnof
fats
attache
dtot he
rough
ERi n
the
Golgi
complex

a. Gol
giappar
at us-amemb
ranousor
ganel
let
hatp
ackagesands
ort
snewl
ysy
nthes
ized
sec
retor
yp roteins

a. Ly
sos
ome-or
ganel
lewhi
chc
ont
ainsd
iges
tiv
eenzy
mes

e.Mi
toc
hond
rion-s
emi
aut
onomouseukar
yot
icc
ell
organel
le

-Si
teofr
esp
irat
ion

-Cons
ist
sofanout
ermemb
raneandac
onv
olut
edi
nnermemb
rane

-Si
teofATPp
rod
uct
ionwi
thi
nthec
ell

a. Mi
crobod
y -organell
ewi t
hinac el
lcont
aini
ngs
pec
ial
izedenzy
meswhos
efunc
tionsi
nvol
ve
hy
drogenp eroxide(p
eroxisome)
b. Mi
crotubules
-c omposedoft ub
uli
n

h.Mi
crof
il
ament
s-c
omp
osedofac
tin

-Bot
h(gandh)ar
einv
olv
edi
ncel
lul
armov
ement

a. I
nterc
ell
ular
-incl
udesflagel
laandcil
ia
b.Intrac
ell
ular
-c y
toplas
mi cst
r eami
ng

Pl
antc
ellor
ganel
les
:

-Chl
orop
las
t-i
nvol
vedi
nphot
osy
nthes
is

-Cent
ralv
acuol
e-p
rov
idess
upp
ortt
othep
lantv
iaos
mot
icp
res
sur
e

-Cel
lwal
l-c
omp
osedofc
ell
ulos
e,whi
chp
rov
idesext
ras
trengt
handr
igi
dit
y

i
.Sp
eci
ali
zedp
rot
ozoanc
ellor
ganel
le:

-Contrac
til
evac
uol
e-us
edt
omai
ntai
npr
operos
mot
icp
res
sur
eands
ecr
eteswas
teand
exces
sH2O
 -Twot
ypesofnuc
lei

1)Mac
ronuc
leus
-inv
olv
edi
nas
exual
rep
rod
uct
ion

2)Mi
cronuc
leus
-inv
olv
edi
nsexual
rep
rod
uct
ion 

Chemi
calBond
s:

I
.4t
ypesofmol
ecul
esmakeupc
ell
s:

1)Car
bohy
drat
es

2)Li
pid
s

3)Pr
otei
ns

4)Nuc
lei
cac
ids

I
I.Bi
ologi
calmac
romol
ecul
esar
ehel
dtoget
herb
ysev
erald
iff
erentt
ypesofb
ond
s:

1)I
oni
cbond
-at
rans
ferofel
ect
rons

2)Cov
alentb
ond
-thes
har
ingofel
ect
rons

3)H-bond
s-weakattr
act
ionwhenH+s
erv
esasab
rid
geb
etween2el
ect
ronegat
iveat
omsb
yac
oval
ent
bondandelec
tros
tat
icat
tract
ion

4)Nonp
olaras
soc
iat
ions
-hy
drop
hob
icv
s.Hy
drop
hil
ic

5)Vand
erWaal
s-amoment
aryd
ipol
ethatwi
llaf
fec
ttheel
ect
rond
ist
rib
uti
onofnei
ghb
ori
ngmol
ecul
es

Ac
idsandBas
es:

Lewi
sdef
ini
tion:

1. Acid-asub st
ancethatcant akeupanel
ect
ronp
airtof
ormac
ovalentb
ond
2. Base-as ubstanc
et hatcand onat
eanel
ectr
onpai
rtofor
macov
alentbond
3. H2Od i
ssociatesi
ntoH+ionsandOH-
4. [H+]+[OH-]=1x10-14moles/
liter(M)
5. pH=-l og10[H+]
6. AcidpHisf rom0t o7
7. Basep Hisf rom7to14

-Condens
ationreac
tion-whent
womol
ecul
esar
ecomb
inedi
ntoonemol
ecul
ewi
tht
her
eleas
eofone
watermolec
ule

-A+B==C+H2O

Ex:2ami
noac
idsar
ejoi
nedt
oget
hert
ofor
mad
ipep
tid
emol
ecul
e

-Hy
drol
ysi
sreac
tion-whenonemol
ecul
eisb
rokeni
ntot
womol
ecul
eswi
tht
head
dit
ionofwat
ermol
ecul
e
-C+H2O==A+B

Ex:d
isac
char
idemal
tos
e+wat
er==2gl
ucos
emol
ecul
es

Reac
tiv
eOr
gani
cMol
ecul
es:

1.Hydroxylgroup-strongl
ypol
arandhi
ghl
yreac
tiv
e

2.Car
bony
lgr
oup-weakl
ypol
arandhi
ghl
yreac
tiv
e

3.Al
dehy
de

4.Ket
one

5.Car
boxy
lgr
oup-s
trongl
ypol
arandac
tsasanac
id 

6.Ami
nogr
oup-p
olarandac
tsasab
ase

7.Phos
phat
egr
oup-ac
idi
candp
olar

8.Sul
fhy
dralgr
oup-r
ead
ilyoxi
dized

-Twos
ulf
hyd
ral
group
scanb
ondt
oget
hert
ofor
mad
isul
fi
deb
ond

Car
bohy
drat
es:

A. Func
tion:

1. Storeenergy(starc
hesi npl
ants/glycogeninani
mal
s)
2. Provi
desrigi
dit
yt oplantcel
ls(
cell
ulos
e)
3. Invol
vedincell
-cel
lcommunicati
on(glycoprot
eins
)

B. St
ruc
tur
e

-Car
bohy
drat
eshav
eac
har
act
eri
sti
ccont
entofC,H,Oat
omsi
nther
ati
oof1C:
2H:
1O

1)Monos
acc
har
idei
sthes
ubuni
tofac
arb
ohy
drat
e

2)Di
sac
char
idec
ont
ains2monos
acc
har
ides
ubuni
ts

3)Ol
igos
acc
har
idec
ont
ains2-10monos
acc
har
ides
ubuni
ts

4)Pol
ysac
char
idec
ont
ains>10monos
acc
har
ides
ubuni
ts

C. Mostcarb
ohy
drat
esub
uni
tsc
ont
ains3c
arb
ons(
tri
ose)
,5c
arb
ons(
pent
ose)
,or6c
arb
ons
(hexos
e)

gl
ucos
e-gl
ucos
e-gl
ucos
e

D.2c
ommonmonos
acc
har
idesar
e:
f
ruc
tos
eandgal
act
ose 
 

E. Di
sac
char
ide=2monos
acc
har
ides
ubuni
tsl
inkedt
oget
her

-Ex:mal
tos
e=2gl
ucos
emol
ecul
esl
inkedt
oget
her

 
-Gl
ycos
idi
cbond=i
stheb
ondb
etween2c
arb
ohy
drat
esub
uni
tsf
ormedb
ytheel
imi
nat
edofwat
er

F. Examp
lesofPol
ysac
char
ides
:

1)Cel
lul
ose-c
ompr
isesplantc
ellwal
ls
;mol
ecul
ecomp
osedofr
epeat
ingB-gl
ucos
euni
ts(
monomer
s)hel
d
toget
herbyB1=4l
inkages

2)Star
ch-(pr
imarystor
agec ompoundi
npl
ant
s)i
samac
romol
ecul
ecomp
osedofr
epeat
ing-gl
ucos
e
uni
tsheldt
ogetherb
y1=4linkages

3)Gl
ycogen-(
primarys
t oragecomp
oundi
nani
mal
s)i
sab
ranc
hedmac
romol
ecul
ecomp
osedofr
epeat
ing
1=4and1=6gl
ycosid
icl
inkages

Suc
ros
e:

Lac
tos
e:

-Mostmonosac
charidescanexi
sti
nalter
nati
vef
ormswhenmol
ecul
es,whi
char
eat
tac
hedt
othec
arb
on
chai
n,canbeorient
edi ndi
ffer
entpos
iti
ons

-St
ereoi
somer
s-t
womol
ecul
es,whi
chhav
ethes
amemol
ecul
arf
ormul
aandt
hes
amec
hemi
calf
ormul
a
andp
hys
icalp
rop
ert
ies
,butar
edi
ffer
enti
nthes
pat
ialar
rangementofat
oms

-Mos
tcar
bohy
drat
esexi
sti
nDandLf
orms

Li
pid
s:

A.Defini
tion-fat
sorf at
-li
kesubst
ancesthatar
eins
olub
lei
nwat
erands
olub
lei
nnonp
olars
olv
ent
sli
ke
acetone,ether
,chlor
oformandbenzene.

B.Func
tion:

1)Pr
imar
ycomp
onentofc
ellmemb
ranes

2)St
oreener
gy

C.Ther
ear
e3t
ypesofl
ipi
ds:neut
rall
ipi
ds,p
hos
phol
ipi
ds,ands
ter
oid
s

D.Neut
rall
ipi
ds(
fat
sandoi
ls
)

1)Comp
osedoff
att
yac
idsandgl
ycer
ol(
alc
ohol
)

2)Fattyac
idi
salong,unb
r anc
hedchai
nofc
arb
onat
omsat
tac
hedb
yhy
drogenandot
her
group
sandaterminalc
arboxylgr
oup

3)CH3(
CH2)
nCOOHs
atur
atedf
att
yac
ids
inc
ethec
arb
onshav
ethemaxi
mump
oss
ibl
e#ofHat
oms

4)CH3(
CH2)
nCH=CH(
CH2)
nCOOHuns
atur
atedf
att
yac
idb
ecaus
eoft
heoned
oub
leC-Cb
ond
.

5)St
ruc
tur
eofneut
rall
ipi
ds

-Gl
ycer
olhas3OHgr
oup
seac
hofwhi
chi
sat
tac
hedt
oaf
att
yac
id

E.Phos
phol
ipi
ds-p
rimar
yli
pid
sinc
ellmemb
ranes

-Mos
tcommonp
hos
phol
ipi
disap
hos
phogl
ycer
ide

-2f
att
yac
ids+gl
ycer
ol+p
hos
phat
egr
oup

-Oneendi
shy
drop
hob
ic;t
heot
herendi
shy
drop
hil
ic=c
all
edamp
hip
athi
c(amp
hip
hil
ic
)

-Tos
ati
sfyt
hes
esol
ubi
li
typ
rop
ert
ies
,phos
phol
ipi
dsar
ranget
hems
elv
esi
ntoal
ipi
dbi
lay
er

-Thel
ipi
dbi
lay
eri
stheb
asi
car
rangementoft
hec
ellmemb
rane

F.St
eroi
ds

-Bas
edonaf
ramewor
kof4c
arb
onr
ing
 

-St
erol
sar
ethemos
tab
und
antgr
oupofs
ter
oid
s

-Anonp
olarsi
dechai
nisattac
hedatoneendoftheri
ngs
truc
tur
eandap
olars
idegr
oup
isat
tachedt
otheopposi
teendoftheri
ngstruc
ture

-R’
isap
olaruni
tandRi
sanonp
olaruni
t

-Thec
omb
inat
ionofp
olarandnonp
olars
idegr
oup
sgi
vesp
hos
phol
ipi
dsd
uals
olub
ili
typ
rop
ert
ies

-Anexamp
leofas
ter
oli
schol
est
erol

-Chol
est
eroli
sani
mpor
tantc
omp
onentoft
hec
ellmemb
ranei
nal
lani
malc
ell
s

-Chol
ester
olal
socanbedeposi
tedinsi
dear
teri
escausi
ngb
loc
kage,whi
chc
ont
rib
utest
o
thedi
seaseart
eri
oscl
eros
is(hardeni
ngoftheart
eri
es)

-Hor
monesar
est
eroi
dsandt
heyp
laymaj
orr
olesi
ncel
lregul
ati
on,c
ell
met
abol
is
m,andc
ell
growt
h

 
I.Pr
otei
nsc
arr
youtmanyc
ell
ularf
unc
tions
:

1)Pr
ovi
dec
ell
ulars
upp
ort(
cyt
oskel
eton:mi
crot
ubul
es–t
ubul
in;mi
crof
il
ament
s-ac
tin)

2)Asenzy
mes
,theyc
atal
yzec
ell
ularr
eac
tions

3)St
abi
li
zeandc
ont
rolgeneac
tiv
ityv
iai
nter
act
ionswi
thot
herp
rot
einsandnuc
lei
cac
ids(
DNAorRNA)

4)Us
edi
ncel
ltr
ans
por
tandc
ellr
ecogni
tion(
cel
lmemb
rane)

5)I
nvol
vedi
ncel
l-c
ellt
rans
por
tvi
asec
ret
oryp
rot
einsandhor
mones

I
I.Pr
otei
nsar
ecomp
osedofs
ubuni
tst
ruc
tur
esc
all
edami
noac
ids

A. 20maj
orb
iol
ogi
calami
noac
ids

B.Gener
als
truc
tur
eofami
noac
id

C.20ami
noac
ids-c
ommi
ttomemor
y:

1)St
ruc
tur
e

2)Name

3)3l
ett
erab
brev
iat
ion
 4)1l
ett
erab
brev
iat
ion

D.Ami
noac
idsc
anb
eli
nkedt
oget
heri
nchai
nsof2ormor
euni
ts

-Pepti
debond-i
sabondinwhi
chthecar
boxyl
groupofoneami
noac
idi
sjoi
nedt
otheami
nogr
oupofa
secondami
noaci
dvi
aac ond
ensat
ionr
eacti
on

-Pep
tid
e-i
sac
hai
ncomp
osedof2ormor
eami
noac
idsandc
ont
ainsoneormor
epep
tid
ebond
s

-Ex:d
ipep
tid
e=c
hai
ncomp
osedof2ami
noac
ids

-Tr
ipep
tid
e=c
hai
ncomp
osedof3ami
noac
ids

-Pol
ypep
tid
eisanami
noac
idc
hai
ncomp
osedof3ormor
eami
noac
ids

-Theami
noac
ids
equenc
eofap
oly
pep
tid
echai
nisc
all
edt
hep
rimar
yst
ruc
tur
eofap
rot
ein

E.Secondarystr
uctureofpr
oteins-ist
hec
onf
ormat
ioni
mpos
edont
hep
oly
pep
tid
echai
nby
hydrogenbond
ingbetweenaminoaci
ds

-Ther
eexi
stsp
hys
icalc
ons
trai
ntsont
her
otat
ionoft
heal
phac
arb
onat
omst
hatf
lankt
hep
ept
ideb
ond

-Ithasb
eendeter
minedt
hatt
her
ear
eonl
y2or3s
tab
lear
rangement
sofami
noac
idswhi
chc
onf
ormt
o
thes
eres
trai
nts

1. Al
phaheli
x
2. Betastr
ands(s
heet
s)
3. Randomcoil

-Thes
ear
rangement
scomp
oset
hes
econd
arys
truc
tur
eofap
oly
pep
tid
echai
n

-Second
arystr
uctur
e-i
sthear
rangementofal
phahel
ic
es,b
etas
heet
s,andr
and
omc
oil
sina
pol
ypepti
dec
hain

1)Alphahel
ix-commonst
ructur
almoti
fofap olyp
epti
dec
hai
ninwhi
cht
hel
inear
sequenceofami
noacid
sfold
sintoari
ght-handedhel
ix

-Hel
ixi
sst
abi
li
zedb
yint
ernalhy
drogenb
ond
ingb
etweenb
ackb
oneat
oms

2)Betasheet-commons
truct
ural
motifofapolyp
eptidechai
n,whi
chi
scomp
osedof
beta,s
trandsthatar
eori
ent
edinanantip
aral
lelfas
hion

-St
abi
li
zedb
yint
ernalhy
drogenb
ond
s

-Bet
ast
rand-i
sanext
end
edzi
gzagar
rangementofami
noac
idsi
nap
oly
pep
tid
echai
n

-Bet
abar
rel-i
sac
yli
ndr
icalar
rangementofb
etas
heet
s

-Examp l
eofap rot
einthatisc
ompos
edp ri
maril
yofbet
as heet
si st
he
si
lkproteinsec
retedbysil
kworms(cont
ribut
est ot
hehighstrengt
hof
si
lkfibers)
 3)Rand
omc
oil-ani
rregul
arc
onf
igur
ati
onofami
noac
idswi
thi
nap
oly
pep
tid
echai
n

-Us
ual
lyc
omp
osedofp
rol
ine-c
annotf
iti
ntoanal
phahel
ixorb
etas
heet

-Al
lowst
hep
rot
eint
obendandf
lex

-Al
lowst
hep
rot
eint
ocomp
acti
ntoi
tsmos
tst
abl
eener
get
ics
truc
tur
e

F)Ter
tiar
yst
ruc
tur
eofp
rot
eins

-Thethree-d
imens
ional
arr
angementofap
oly
pep
tid
echai
nwi
thi
nap
rot
ein(
monomer
ic
prot
ein)

G)Quat
ernar
yst
ruc
tur
eofp
rot
ein

-Three-d
imens
ionalr
elat
ions
hipb
etween2ormor
epol
ypep
tid
echai
nswi
thi
nac
omp
lex
prot
ein

-Ex:c
oil
edc
oil&t
rip
lehel
ix

-Di
mer=2s
ubuni
ts

-Homod
imer=i
dent
icals
ubuni
ts

-Het
erod
imer=d
ist
inc
tsub
uni
ts

-Mul
ti
mer
icp
rot
ein-c
omp
osedof2ormor
esub
uni
ts(
ident
ical
ord
ist
inc
t)

Nuc
lei
cac
ids
:

I
.Defi
nit
ion-al
arge,c
hai
n-l
ikemac
romol
ecul
econt
aini
ngp
hos
phor
icac
id,s
ugar
,andani
trogenous
b
ase

-2examp
lesar
edeoxy
rib
onuc
lei
cac
id(
DNA)&r
ibonuc
lei
cac
id(
RNA)

a.Sugari
s5-c
arb
ons
ugarc
all
edap
ent
ose

r
ibos
edeoxy
rib
ose

b
.Phos
phor
icac
idi
scomp
osedofoneormor
ephos
phat
egr
oup
s(PO4-)

c
.Ni
trogenousb
ase=2t
ypes

p
uri
nep
yri
mid
ine
 

 1.Twoc
ommonp
uri
neb
ases
,ad
eni
neandguani
ne

6-ami
nop
uri
ne(
adeni
ne)2-ami
no-6-hy
droxy
pur
ine(
guani
ne)

2.Thr
eec
ommonp
yri
mid
ineb
ases
,cy
tos
ine,t
hymi
ne,andur
aci
l

4-ami
no-2-hy
droxy
pyr
imi
dine2,
4-d
ihy
droxy
pyr
imi
dine2,
4-d
ihy
droxy
-5-met
hyl
pyr
imi
dine

(
cyt
osi
ne)(
urac
il
)(t
hymi
ne)

I
I.Nuc
leos
ide-mac
romol
ecul
ecomp
osedofani
trogenousb
asej
oinedt
oap
ent
ose

III
.Nucl
eoti
de-isamac
r omol
ecul
ecomp
osedofani
trogenousb
ase,ap
ent
ose,andl
inked(
est
eri
fied
)to
oneormorephos
phat
egroups

-5’
-ri
bo(
deoxy
rib
o)-nuc
leot
ide

-Phos
phat
eisl
inkedt
othe3’
OHoft
hep
ent
ose=3’
-ri
bo(
deoxy
rib
o)-nuc
leot
ide

I
V.Nomenc
lat
ureofnuc
leos
ides
:

A-d
eoxy
rib
osi
de=d
eoxy
adenos
ineA-r
ibos
ide=ad
enos
ine

G-d
eoxy
rib
osi
de=d
eoxy
guanos
ineG-r
ibos
ide=guanos
ine

C-d
eoxy
rib
osi
de=d
eoxy
cyt
idi
neC-r
ibos
ide=c
yti
dine

T-d
eoxy
rib
osi
de=d
eoxy
thy
mid
ineU-r
ibos
ide=ur
idi
ne
V.Nomenc
lat
ureofnuc
leot
idesi
nDNA

b
ase-d
eoxy
rib
ose-p
hos
phat
e

5’
-dAMP=d
eoxy
adenos
ine-5’
-PO4

5’
-dGMP=d
eoxy
guanos
ine-5’
-PO4

5’
-dTMP=d
eoxy
thy
mid
ine-5’
-PO4

5’
-dCMP=d
eoxy
cyt
idi
ne-5’
-PO4

VI
.Nomenc
lat
ureofnuc
leot
idesi
nRNA

b
ase-r
ibos
e-p
hos
phat
e

5’
-AMP=ad
enos
ine-5’
-PO4

5’
-GMP=guanos
ine-5’
-PO4

5’
-UMP=ur
idi
ne-5’
-PO4

5’
-CMP=c
yti
dine-5’
-PO4

VI
I.Nomenc
lat
ureofnuc
leos
idet
rip
hos
phat
es

ATP=ad
enos
ine-5’
-tr
iphos
phat
e

d
ATP=d
eoxy
adenos
ine-5’
-tr
iphos
phat
e

VI
II.Nuc
lei
cac
idsRNAandDNA

-Nucl
eotidesheldinc
hainsbybri
dgi
ngaphos
p hategroupt
hatextendsbet
weent
he5’
-
carb
onofones ugarwit
ht he3’
-car
bonofasecondsugar(hel
dtoget
herbya
phosphod
iesterbond)

-Pr
oduc
esab
ackb
onec
hai
nofal
ter
nat
ings
ugarandPO4gr
oup
s

-DNAexi
stsi
nad
oub
lehel
ixt
hatc
ont
ains2i
nter
twi
nedc
hai
nsofnuc
leot
ides

-RNAi
ssi
ngl
e-s
trand
ed

Enzy
mes
:

1.Rev
iewt
her
mod
ynami
cs

-Fi
rstands
econdl
awoft
her
mod
ynami
cs

-Rev
ers
ibl
ereac
tions

-Coup
lingr
eac
tions
-St
and
ardf
reeener
gyc
hange

2.Defi
nit
ionofanenzy
me-i
sap
rot
einwhi
chi
ncr
eas
est
her
ateofas
pont
aneousr
eac
tion(
cat
aly
zes
thereact
ion)

a)Lower
stheac
tiv
ati
onener
gyoft
het
rans
iti
ons
tat
e

b
)Reac
tionwoul
dpr
oceedwi
thoutt
heenzy
me

c
)Enzy
mec
annotmakear
eac
tionoc
curt
hatwoul
dnotp
roc
eeds
pont
aneous
lywi
thoutt
heenzy
me

d
)Enzy
mesd
onotal
tert
heequi
li
bri
umofar
ever
sib
ler
eac
tion

e)Enzy
mesi
ncr
eas
ether
ateatwhi
char
eac
tionr
eac
hesequi
li
bri
um

Cl
ass
ifi
cat
ionofenzy
mes
:

1.Oxi
dor
educt
ases-cat
alyzesar
eac
tioni
nwhi
chel
ect
ronsar
eremov
edf
romt
hes
ubs
trat
ear
edonat
ed
di
rect
lytomol
ecul
aroxygen

-Cat
aly
zesoxi
dat
ion-r
educ
tionr
eac
tions

-Ac
tonal
cohol
s,ket
ones
,al
dehy
des
,ami
nes
,et
c.

2.Tr
ans
fer
ase-c
atal
yzet
het
rans
feroff
unc
tional
group
s

-Sul
fhy
dral
,gl
ycos
yl,al
dehy
de,ac
yl,et
c.

3.Hy
drol
ases-c
atal
yzehy
drol
ysi
sreac
tions

-Gl
ycos
idi
cbond
s

-Pep
tid
ebond
s

4.Ly
ases-c
atal
yzet
head
dit
ionofgr
oup
stod
oub
leb
ond
s

-C=C,C=N,C=O

-Ex:APl
yas
esi
nvol
vedi
nrep
air
ingDNA

5.I
somer
ases-c
atal
yzeani
ntr
amol
ecul
arr
ear
rangement

-Cat
aly
zedi
somer
izat
ionr
eac
tion

-I
somer
izat
ion-r
ear
rangementofat
omi
cgr
oupwi
thi
nthes
amemol
ecul
ewi
thoutanyl
ossorgai
nof
at
oms

6.Ligas
es-agroupofenzymesthatcat
alyzereacti
onsinwhi
chabondisf
ormedbet
ween2s
ubs
trat
e
molecul
esus
ingener
gy(ATP)obt
ainedfromthec l
eavageofapyr
ophos
phatebond
-Ex:DNAl
igas
e&RNAl
igas
e

Char
act
eri
sti
csofenzy
mat
icp
rot
eins
:

-Enzy
mescomb
ineb
rief
lywi
thr
eac
tant
sdur
inganenzy
me-c
atal
yzedr
eac
tion(
enzy
me-s
ubs
trat
e
compl
ex)

-Enzy
mesar
erel
eas
edunc
hangedaf
terc
atal
yzi
ngt
hec
onv
ers
ionofr
eac
tant
stop
rod
uct
s

-Enzymesarespec
ifi
cinthei
racti
vit
y;eachenzymecat
aly
zest
her
eac
tionofas
ingl
e
typeofmolec
uleoragroupofcl
osel
yr el
atedmol
ecul
es

-Enzy
mesar
esat
urat
edb
yhi
ghs
ubs
trat
econc
ent
rat
ions

-Manyenzy
mesc
ont
ainnonp
rot
eingr
oup
scal
ledc
ofac
tor
s

-I
nor
gani
ccof
act
ors=met
ali
ons

-Or
gani
ccof
act
ors=c
oenzy
mes(
ex:v
itami
ns)

I
.Ac
t i
vat
ionenergy
:t heener
gyinexcessofthegr
oundst
atethatmustbead
dedtoamol
ecul
ars
yst
em
t
oal
lowac hemi
calreacti
ontost
art(e.g.roc
konac l
if
fmustb
ep us
hedtorol
ldownt
hehi
ll
)

-Onewayt
osup
plyener
gyi
stoheatt
her
eac
tant
s

-Sec
ondwayi
stoad
dac
atal
yst

-Catalys
tformsac omp
lexwit
ht hereac
tant,t
husb
ringi
ngt
he
reac
t antsc
losert
ogethersotheycanreact

-I
nb i
ologi
cals
ystemsacatal
ysti
scal
ledanenzy
me,whi
chl
ower
sthe
ac
tiv
ationenergyofthesy
s t
em

-Gr
aph:

I
I.Threeenzymati
cmechanismswhi
chc
anc
ont
rib
utet
othef
ormat
ionofat
rans
iti
ons
tat
eisa
c
atal
yzedbiol
ogi
calreac
tion

a)Enzy
meb
ringsr
eac
tingmol
ecul
esi
ntoc
los
epr
oxi
mit
y
 b
)Enzy
meor
ient
sreac
tant
sint
opos
iti
onst
oind
ucef
avor
abl
eint
erac
tions

c
)Enzy
mesal
tert
hec
hemi
calenv
ironmentoft
her
eac
tant
stop
romot
eint
erac
tion

-E.
g.i
stoc
reat
eanonp
olarenv
ironment

-Fav
orab
lec
ond
iti
onf
orr
eac
tantnonp
olarmol
ecul
es

I
II.Fac
tor
saf
fec
tingenzy
meac
tiv
ity

a)Sub
str
atec
onc
ent
rat
ion

b
)Enzy
mei
nhi
bit
ion

-Comp
eti
tiv
e

-Nonc
omp
eti
tiv
e

c
)Temp
erat
ure-op
timumt
emp
.40C

-I
ftemp
.inc
reas
eswi
lld
enat
uret
hep
rot
eins

d
)pH-op
timump
H7f
ormos
tenzy
mes

I
V.Sub
str
atec
onc
ent
rat
ion-r
eac
tant
s(s
ubs
trat
es)  p
rod
uct
s

-Ast
her
eac
tionp
roc
eed
s,t
hec
onc
ent
rat
ionofs
ubs
trat
edec
reas
eswi
tht
ime

-Ifweincr
easetheconcent
rat
ionofsub
str
ate,wewi
lli
ncr
eas
ethe
rateofanenzymati
creacti
ontoapoi
nt

-Fr
omt
hisp
oint
,ifad
dmor
esub
str
ate,t
her
ateoft
her
eac
tionwi
llnoti
ncr
eas
e

-Theenzy
mei
ssai
dtob
esat
urat
edwi
ths
ubs
trat
e

-Thi
sef
fec
tiss
eenwi
thal
lenzy
mes

-Gr
aph:

 
-PhenomenonledMichael
isandMenten(1913)tot heexpl
anat
ionthatt
heenzyme(
E)andthes
ubstr
ate
(S)formar ev
ersi
blecomplexES.TheESt henb
r eaksdowntogivethepr
oduc
tPandthefr
eeenzy
me

-Theyd
eri
vedanexp
lanat
iont
odes
cri
beenzy
mer
eac
tions

7.Der
ivat
ionoft
heMi
chael
isMent
enEquat
ion:

Enzy
mei
nhi
bit
ion:

-Modelforanenzy
me-cat
alyzedr
eacti
onr
equi
rest
hatt
heenzy
meands
ubs
trat
efor
mar
ecogni
zab
le
chemic
alcompl
exES(tr
ansit
ionstat
e)

-I
ngener
al,enzy
mesar
emuc
hlar
geri
nsi
zet
hans
ubs
trat
emol
ecul
es

-Por
t i
onoft
heenzy
met
hatc
omp
lexeswi
tht
hes
ubs
trat
ear
ecal
ledt
heac
tiv
ecent
er(
sit
e)oft
he
enzyme

-Iti
snotknownexac
tlyhowenzy
mesl
owert
heener
gyr
equi
redt
ofor
mthet
rans
iti
ons
tat
eorES
comp
lex

-Wedoknowt hatt hecomplexexis

t sbyanexper
imentcompl
etedbyLernerandSchultzwhogener
at ed
Ab’
sagains
tmol eculeswhichcl
oselyresemb
leatheoret
ical
transi
tions
t at
e(transi
tionstat
eanalogs-
actasenzymesb ycataly
zingreactions=abzy
mes )

-Agoodamountofchemic
ali
nfor
mat
ionc
onc
erni
ngt
heac
tiv
esi
tesofenzy
meshasb
eenob
tai
nedb
y
stud
yingenzy
meinhibi
tor
s

-Chemi
cali
nhi
bit
or-i
sas
ubs
tanc
ethatr
epr
ess
esors
top
sac
hemi
cal
reac
tion
-I
nhi
bit
ion-r
educ
tioni
nther
ateofenzy
mat
icac
tiv
ity

E+S  ES  E+P

E+I  EI nop

rod
uct
s

a)Comp
eti
tiv
einhi
bit
ion-

b
)Nonc
omp
eti
tiv
einhi
bit
ion-

1.Competi
tiveinhi
bit
ion-t heinhib
itionofenzymeactiv
itycausedbythecompet
iti
onofaninhi
bit
orwith
asubstrat
ef ortheactiv
e( cat
alytic)siteontheenzy
me;imp ai
rmentofthefuncti
onofanenzymedue
toitsr
eactionwithas ubst
ancec hemi c
allyr
elat
edtoitsnor
mals ubst
rate

-Ver
ycommons
ituat
ioni
nthes
tud
yofd
rugac
tion

-Manyd
rugswor
kbyc
omp
eti
ngwi
tht
henor
mals
ubs
trat
emol
ecul
esf
ort
heac
tiv
esi
teofenzy
mes

-Li
neweav
er-Bur
kep
lot
:

 
 

2.Noncompetiti
vei
nhi
biti
on-inhi
bit
ionofenzy
meac t
ivi
tybyasubs
tancethatdoesnotcomp
etewi
tht
he
normalsub
st r
atefortheact
ivesi
teandthuscannotbered
ucedbyi
ncreas
ingthesubstr
ate
concent
ration

-Li
neweav
er-Bur
kep
lot
:

 
 

 
Regul
ati
onofEnzy
mat
icAc
tiv
ity
:

-I
nli
vingc
ell
s,c
hemi
calequi
li
bri
aforr
eac
tionsar
esel
dom,i
fev
er,r
eac
hed

-Duet
othef
actt
hatc
ell
ularc
hemi
calr
eac
tionsar
ecoup
ledt
ofor
mmet
abol
icp
athway
s

A  B  C  D  E

-Thr
eemaj
orknownmec
hani
smsb
ywhi
chenzy
meac
tiv
iti
esap
peart
ober
egul
ated
:

a)Changei
nther
ateofs
ynt
hes
isoft
heenzy
me

-I
nduc
tionoft
heenzy
me&r
epr
ess
ionoft
heenzy
mec
ont
rib
utet
ogener
egul
ati
on

b
)Feedbac
kinhib
iti
onoftheenzyme-c el
lularcontrol
mechanis
mb ywhi
chtheend
p
roduc
tofas eri
esofmetabol
icreac
tionsinhibi
tstheacti
vit
yofanearli
erenzymein
t
hemetaboli
cpathway
;thus,whentheendp r
oductaccumul
ates,i
tsfur
therproduc
tion
c
eases

c
)Al
los
ter
icr
egul
ati
on(
inhi
bit
ion)
:

-Occ
ursbyrev
ers
ibl
ecomb
inat
ionofs
ubs
tanc
eswi
ths
itesont
heenzy
meot
hert
hant
he
act
ivesi
te

-Enzymei
scal
ledanal
los
ter
icenzyme-anenzymewhoseact
ivesi
tecan
bealt
eredbyt
heb i
ndi
ngofasmallmol
ecul
eatanon-ov
erl
appings
ite

-Enzy
mec
anb
eac
tiv
atedb
ythi
sbi
ndi
ng=al
los
ter
icac
tiv
ati
on

-Enzy
mec
anb
einhi
bit
edb
ythi
sbi
ndi
ng=al
los
ter
ici
nhi
bit
ion

RNAb
asedenzy
mes(
rib
ozy
mes
):

-Fi
rstd
isc
over
edi
nthep
rot
ozoanTet
rahy
mena

-RNAmol
ecul
einv
olv
edi
nsp
lic
ing(
ormod
ify
ing)RNAi
nter
med
iat
est
ruc
tur
es

-Di
scov
eredb
yTomCec
h

DNAs
truc
tur
e:
-St
ruc
tur
eofDNAwasd
educ
edb
yx-r
ayd
iff
rac
tionandp
rop
osedb
yWat
sonandCr
ick

8c
har
act
eri
sti
cs:

1)Cont
ains2nuc
leot
idec
hai
nswhi
chwi
ndi
ntoar
ight
-hand
edd
oub
lehel
ix

2)Bac
kbonei
scomp
osedofal
ter
nat
ings
ugarandp
hos
phat
egr
oup
ssep
arat
edb
y1.
1nn

3)Sp
acei
sfi
ll
edb
yap
uri
ne:p
yri
mid
ineb
asep
air
,whi
chl
iesi
naf
lat
,pl
anep
erp
end
icul
art
otheb
ackb
one

4)Eac
htur
noft
hed
oub
lehel
ixi
s10b
p

5)Theb
par
ehel
dtoget
herb
yH-b
ond
s

6)Ther
ear
e2s
urf
acegr
oov
esont
hehel
ix,maj
orgr
oov
eandami
norgr
oov
e

7)Thenuc
leot
idec
hai
nsoft
hehel
ixr
uni
nop
pos
ited
irec
tions

5’
 3’

3’
 5’

8)Thi
santi
paral
lelarr
angementr
equirest
hatanewDNAc
hai
nbei
ngc
opi
edf
roman
exist
ings
trandmus truni
ntheoppos
itedi
rec
tion

-Par
ents
trand=t
emp
lat
e

-News
trand=c
omp
lement
arys
trand

Mod
ifi
cat
ionst
oDNASt
ruc
tur
e:

1.Al
ter
nat
iveDNAf
orms(
B-DNA)

-Lef
t-hand
edhel
ix(
Z-DNA)
-inv
olv
edi
ngenet
rans
cri
pti
onandgener
ecomb
inat
ion

2.Chemi
calmod
ifi
cat
ion

-5met
hylc
ytos
ine-i
nvol
vedi
ngener
egul
ati
on

-Themet
hyl
ati
onofDNAl
ead
stoas
hutd
ownoft
rans
cri
pti
on

3.Sup
erc
oil
ing-c
omp
act
ionofDNA

-Supercoi
lsi
nducedbyagroupofenzy
mescal
ledtop
ois
omer
ases
-anenzy
met
hat
changestheextentofsup
ercoi
li
ngoftheDNAcompl
ex

-Thes
eenzy
mesc
anal
sor
emov
esup
erc
oil
sorr
elaxt
hem

-Sup
erc
oil
ingp
lay
samaj
orr
olei
ngener
egul
ati
on,t
rans
cri
pti
on,andDNAr
epl
ic
ati
on

Pr
otei
nsAs
soc
iat
edwi
thDNA:
A.Hi
stones-b
as i
cprotei
nsric
hinar
gini
neandl
ysi
net
hatoc
curi
ncl
oseas
soc
iat
ionwi
tht
henuc
learDNA
ofmosteukaryoti
corganis
ms

1.Maj
ort
ypesofhi
stones-H1,H2A,H2B,H3,andH4

-Thel
astf
ourareas
soc
iatedwi
theachot
herandt
oget
herwi
thDNA
theyf
ormastr
uctur
ecall
edanucl
eos
ome

2.Nuc
leos
ome-t
hef
unc
tionaluni
tofc
hromat
ini
neukar
yot
es

-Nuc
leos
omesp
ackDNAi
nas
tab
lec
oil
edf
orm

-Cont
rib
ut etogener
egul
ati
on(changess
truc
tur
edur
ingp
roc
essof
DNArepl
icati
on,andt
rans
cri
pti
on)

3.Nuc
leos
omes
truc
tur
e

4.Corepart
icl
e-ofanuc
leosomeconsi
stsof2eac
hofthefourcorehi
stoneprot
eins2
H2A,2H2B,2H3,and2H4p l
us2lefthandtur
nsofDNAthatiswoundaroundt
he
prot
eins

5.Li
nker
-ist
heDNAt
hatl
inksonenuc
leos
omet
othenext

6.H1as
soc
iat
eswi
thDNAatt
heendent
eri
ngandl
eav
ingt
hec
orep
art
icl
e

 
 

B.Nonhi
stonePr
otei
ns-p
rot
einsot
hert
hanhi
stonest
hatar
eas
soc
iat
edwi
thDNAi
nchr
omat
in

1.Ty
pesofnonhi
stonep
rot
eins

a)Tr
ans
cri
pti
onr
egul
ator
yfac
tor
s-p
rot
einsr
egul
ati
ngi
nthep
roc
essoft
rans
cri
pti
on

b
)Enzymescatal
yzi
ngreact
ionsoft
ransc
rip
tion,r
epl
ic
at i
on,
r
ecombi
nati
on,DNArep
air,andmodi
fic
ati
onofDNAandc hromos
omal
p
rotei
ns

c
)Pr
otei
nsc
ont
rib
uti
ngt
omai
ntenanc
eofc
hromat
ins
truc
tur
e

Or
gani
zat
ionofNuc
leos
omeswi
thChr
omat
inFi
ber
s:

-Nuc
leos
omesf
orms
olenoi
dst
ruc
tur
est
ofur
therc
omp
actc
hromat
in

-Thi
sst
ruc
tur
edep
end
sonH1

-I
nhumans1met
erofDNAi
scomp
aced104f
t old
Chr
omat
ini
nInt
erp
has
enuc
leus
:

-Euc
hromat
in-l
oos
elyp
ackedr
egi
onsofc
hromat
inf
iber
s=wher
egenesar
eexp
res
sed

-Het
eroc
hromat
in-d
ens
elyp
ackedr
egi
onsofc
hromat
inf
iber
s=i
nac
tiv
egenes

DNARep
lic
ati
on:

-Thep
roc
esswher
ethep
arent
alDNAmol
ecul
eisd
upl
ic
atedi
nto2exac
tcop
ies

-Pr
oces
soc
cur
sbyas
emi
-cons
erv
ati
vemec
hani
sm

-Semi-cons
ervat
iver
ep l
ic
ati
on-ist
hep r
oducti
onofad
oub
le-s
trand
edDNAmol
ecul
e
contai
ningonenewstrandandonepar
entals
trand

-I
ll
ust
rat
edb
yMes
els
onandSt
ahl

15
-Theyl
abel
edDNAi
ndi
vid
ingb
act
eri
alc
ell
swi
thani
sot
opeofni
trogen( N)

-Remov
elab
elandgr
ewc
ell
in14N

-Afteronegener
at i
on,i
solat
edDNAandf
oundt
hatt
heDNAwasc
omp
osedofones
trand
of14Nandonestrandof15N

14
-IfDNAr
epl
ic
atedb
yac
ons
erv
ati
vemec
hani
sm,DNAwoul
dexi
sti
ntwof
orms( Nand
15
N)

Ov
erv
iewofMec
hani
sm:

1.DNAr
epl
ic
ati
oni
scat
aly
zedb
yanenzy
meDNAp
oly
mer
ase

2.DNAp
oly
mer
aser
equi
resas
hor
tst
ret
chofnuc
leot
idest
oini
tiat
erep
lic
ati
onc
all
edap
rimer

3.Rep
lic
ati
onofnews
trandoc
cur
sina5’
 3’
dir
ect
ion

4.DNApol
ymer
asebind
stot
he3’
OHgr
oupoft
hes
ugaroft
hep
rimerandr
ecogni
zest
he
fi
rstbas
etobecop
ied

5.Bindi
ngofthebasefavorst
heli
nkagebetweenthe3’OHgr
oupofthepr
imerandt
he
innermost(
alp
ha)phos
p hat
egroupboundtothe5’
c ar
bonofthei
ncomi
ngbas
e

-Theb
etaandgammaPO4ar
eremov
ed

-Thealphaphosphat
eisboundt
ot heoxygenofthe3’OHgr ouponthe
sugarofthep r
imercreat
inga5’ 3’p
hosphodi
esterbondorli
nkage
betweenthep r
imerandtheadd
ednuc l
eotid
e

-Thi
sisal
inkageb
etween2al
cohol
sandaPO4gr
oup

6.DNAp
oly
mer
asemov
est
othenextb
aseont
het
emp
lat
eandr
epeat
sst
eps4and5
 -Dur
ingt
hisp
roc
ess
,eac
hnuc
leot
idei
sad
dedt
oanexp
osed3’
-OHgr
oup

-A3’
-OHgr
oupi
sal
way
spr
esentatt
henewes
tendoft
hegr
owi
ngc
hai
n

-Sy
nthes
isp
roc
eed
sina5’
 3’
fas
hion

Fund
ament
alFeat
uresofDNARep
lic
ati
on:

1.Twonuc
leot
idec
hai
nsoft
emp
lat
eDNAd
oub
lehel
ixmus
tunwi
ndands
epar
atep
riort
orep
lic
ati
on

2.Unwi
ndi
ngandr
epl
ic
ati
onmus
tpr
oceedi
nthes
amed
irec
tion

3.Repl
icat
ionofthe3’
 5’t
emp
lat
eoc
cur
sina5’
 3’
dir
ect
ion,whi
chp
rod
ucesa
cont
inuous,orl
eadi
ngstr
and

4.Rep
lic
ati
onoft
he5’
 3’
temp
lat
eal
sooc
cur
sina5’
 3’
fas
hion

-For
mss
hor
tlengt
hsorOkazakif
ragment
s

-Pr
oduc
esad
isc
ont
inuousorl
aggi
ngs
trand

-Fragment
sar
ethenj
oinedt
oget
herwi
thc
oval
entb
ond
scat
aly
zedb
ytheenzy
meDNA
l
igase

St
epsi
nDNARep
lic
ati
on:

1.Unwi
ndi
ngofDNAd
oub
lehel
ix

-Cat
aly
zedb
yenzy
mest
hatr
equi
reener
gy(
ATP)c
all
edDNAhel
ic
ase

-s
sDNAr
egi
oni
sthens
tab
ili
zedb
yDNAb
ind
ingp
rot
eins

-unwi
ndi
ngi
nduc
ess
uper
coi
lsi
ntot
heDNAmol
ecul
e

-super
coil
sareremov
edtypeofenzymeDNAtop
ois
omeras
ethat
intr
oducessi
ngl
eordoub
le-st
randedbr
eaksi
ntheDNA

-pri
mer-i
sas hortnuc
leoti
desequence(
oftenRNA)thati
spai
redwit
h
onestr
andofDNAandp rov
idesafree3’
-OHatwhichaDNApol
ymerase
star
tssynthesi
sofanewDNAc hai
n

2.afterunwi
ndi
ng,RNAprimersar
eat t
achedt
oss
DNAt
hrought
heac
tionsofa
spec
iali
zedRNApol
ymeras
e( pr
imase)

-p
rimas
elay
ers5-10nuc
leot
idesi
nlengt
hina5’
 3’
dir
ect
iond
ownas
trand

-p
rimerp
rov
idesaf
ree3’
-OHgr
oupt
hati
snec
ess
aryf
orDNAp
oly
mer
aset
oop
erat
e

3.DNApol
ymer
asethendi
rec
tst hei
ncor
porat
ionofthepr
operbas
edur
ingt
he5’
 3’
repl
ic
ati
onofthet
emplat
estrands(l
eadi
ngandlaggi
ngs
trands
)
 -inaddi
ti
ont
oit
spol
ymer
izat
ionf
unc
tion,DNAp
oly
mer
aseal
sohasap
roof
read
ing
funct
ion

-DNAp
oly
mer
ases
ear
chesf
orDNAb
pmi
smat
ches
)

-ac
cur
acyofDNAr
epl
ic
ati
oni 107b
s1/ ases

Pr
okar
yot
icDNAp
oly
mer
ases
:

-IandI
I=f
unc
tioni
nDNAr
epai
r

-I
II=DNAr
epl
ic
ati
on

Eukar
yot
icDNAPol
ymer
ases
:

-=DNAr
epl
ic
ati
on

-=DNAr
epai
r

-=DNAr
epl
ic
ati
oni
nmi
toc
hond
riaandc
hlor
opl
ast
s

-=DNAr
epl
ic
ati
on

-=DNAr
epai
r

-p
roof
readf
unc
tion-c
arr
iedouti
na3’
 5’
ora5’
 3’

-exonuc
leas
e-enzy
met
hatr
emov
esnuc
leot
idesoneatat
imef
romt
heendofanuc
leot
idec
hai
n

-end
onuc
leas
e-anenzy
met
hatc
atal
yzest
hec
leav
ageofDNAatas
pec
ifi
cint
ernal
sit
e(r
est
ric
tion
enzy
me)

-DNAc
anexi
stasac
irc
ularoral
inearmol
ecul
e

-r
epl
ic
ati
onofl
inearendofDNAi
scar
riedoutb
yanenzy
mec
omp
osedofRNAc
all
edat
elomer
ase

-t
elomer
asead
dsr
epeat
ednuc
lei
cac
ids
equenc
est
otheendofDNA

-repeat
ingendsareusedforpr
imersynt
hes
ist
ogener
ated
upl
ic
ateDNA,whi
chc
orr
esp
ond
stot
he
sequenceendofthel
inearDNAmolec
ule

RNA:

1.Tr
ans
cri
pti
on:

-t
hes
ynt
hes
isofmRNA,r
RNA,andt
RNAf
romaDNAt
emp
lat
e

-messengerRNA(mRNA)-i
stheribonuc
lei
cac
id(
RNA)t
hats
pec
ifi
est
heami
noac
id
sequenceforapar
tic
ularpol
ypep
tidechai
n

-s
sRNA
-r
ibos
omalRNA(
rRNA)
-ist
her
ibonuc
lei
cac
idofv
ari
ouss
izest
hatmakesupp
artoft
her
ibos
omes

-c
ons
tit
utesupt
o90%oft
het
otal
RNAofac
ell

-s
sRNA,wi
thhel
ic
alr
egi
onsf
ormedb
ybpb
etweenc
omp
lement
aryr
egi
onswi
thi
nthes
trand

-tr
ansf
erRNA(
tRNA)
-ist
her
ibonuc
lei
cac
idi
nvol
vedi
ncar
ryi
ngami
noac
idst
other
ibos
omesd
uri
ng
tr
ansl
ation

-f
oreac
hami
noac
idt
her
ear
eoneormor
ecor
res
pond
ingt
RNA’
sthatc
anb
indi
tsp
eci
fic
all
y

2.t
heenzy
met
hatc
atal
yzest
rans
cri
pti
oni
scal
ledRNAp
oly
mer
ase

3.eac
hRNAistrans
cri
bedf
romDNAi
nap
rec
urs
orf
orm=(
hnRNA)het
erogeneousnuc
learRNA,p
re-
mRNA,orp
re-RNA

4.t
hec
onv
ers
ionofhnRNA mRNA,r
RNA,andt
RNAi
scal
ledRNAp
roc
ess
ing

-s
tep
s:

1.ad
dit
ionofa5’
cap

2.ad
dit
ionofa3’
pol
y-At
ail

3.s
pli
ci
ngoutofi
ntr
ons

4.RNAs
truc
tur
e

-s
ingl
est
rand
edmol
ecul
ecomp
osedofr
ibonuc
leot
ides

-mol
ecul
ecanf
ormav
ari
etyofd
oub
le-hel
ic
als
truc
tur
es-whi
chp
layamaj
orr
olei
ngeneexp
res
sion

-s
truc
tur
es:

hai
rpi
nst
eml
oop

-d
oub
le-hel
ic
alhai
rpi
nst
ruc
tur
esc
ont
aini
nver
tedr
epeat
s(I
R)

-whi
char
esy
mmet
ric
all
yrev
ers
eds
equenc
es(
pal
ind
rones
equenc
es)

-p
rimar
yst
ruc
tur
e-s
equenc
eofni
trogenousb
ases

-s
econd
arys
truc
tur
e-d
oub
le-hel
ic
als
truc
tur
eder
ivedf
romb
ase-p
air
ingofi
nver
tedr
epeat
s

-t
ert
iar
yst
ruc
tur
e-3-Ds
truc
tur
esuc
hasr
RNAandt
RNA
 -2oand3ostruc
t uresareimp
or t
antasr ec
ogni
tions
itesf
orenzymati
c,str
uctur
al,and
regul
atoryproteinsacti
veatalllevel
sofRNAf unct
ionfromt
ranscr
ipti
on,pr
ocessi
ng,
andRNAt ransportthroughproteintransl
ati
on

5.RNAt
rans
cri
pti
on:

-r
equi
res
:

1)aDNAt
emp
lat
e

2)Mg2+orMn2+

3)FourRNAnuc
leos
idet
rip
hos
phat
es(
ATP,CTP,GTP,UTP)

a)RNApolymeras
eb i
ndstotheDNAt emp
lat
eand
recogni
zesthefirs
tbase(ex.Guani
ne)

b)RNApoly
meraserec
ognizesandbi
ndstoCTP(b
pwi
th
guani
ne);und
ergoesaconformati
onalc
hange

c
)RNAp
oly
mer
aser
ead
sthenextb
ase(
adeni
ne)

d
)RNAp
oly
mer
aseb
ind
sUTP(
bpwi
thad
eni
ne)

e)
RNAp
oly
mer
asec
atal
yzest
hel
inkageb
etweenCTPandUTP

-t
ermi
nalt
wop
hos
phat
esofUTP(and)ar
eremov
ed

-al
phap
hos
phat
ebi
ndst
otheOHatc
arb
on3oft
her
ibos
esugar

-enzymereact
ioncreatesaphosp
hod i
esterl
inkageb
etweent
he3’
car
bonoft
hef
irs
t
sugarandthe5’car
b onofthesecondsugar

f
)rep
eats
tep
sb ef
ort
henextb
ase

g)atoneendoftheDNAt empl
ate,newlysynthes
ized
RNAmol ec
uleandtheenzymearereleasedfr
omt heDNA
templat
e,andtransc
ript
ioni
st er
minated

-t
hef
irs
tnuc
leot
ider
etai
ns3p
hos
phat
es(
li
nkedt
othe5’
car
bonofs
ugar
)==5’
endoft
hemol
ecul
e

-l
astnuc
leot
idehasanOHgr
oupatt
he3c
arb
onoft
hes
ugar
==3’
endoft
hemol
ecul
e

-si
ncethe5’c
arbonmar
kst heb
egi
nni
nganda3’OHmar
kst
heendofaRNAmol
ecul
e
tr
anscr
ipti
oniss
aidtoproc
eedina5’
 3’d
irec
tion

6.Thr
eep
has
esoft
rans
cri
pti
on:

1.ini
ti
ati
on-at
tachmentofRNApol
ymer
asetot
heDNAt
emp
lat
eandb
ind
ingb
ythe
enzymeofthefi
rstnucl
eoti
dei
nthenewstr
and
2.el
ongat
ion-r
eac
tioni
nwhi
chRNAnuc
leot
idesar
ead
deds
equent
ial
lyac
cor
dingt
otheDNAt
emp
lat
e

3.terminat
ion-endofRNApol
ymeri
zati
onwhereRNApol
ymer
aseandt
henewl
y
synthes
izedtranscr
iptar
erel
easedfr
omthetempl
ate

Tr
ans
cri
pti
on:

I
.Ini
tiat
ion:

-TFI
IDi
sac ompl
exmult
imer
icpr
otei
n,whic
hincludesonepol
ypepti
decal
ledt
heTATA-
bi
ndi
ngpr
otein(
TBP)whi
chbi
ndstotheTATAsequenceinthepromoter

-up
str
eamDNAs
equenc
es:

-t
rans
cri
pti
ons
tar
tsat+1ont
heDNAt
emp
lat
e

a)
TATAb
oxf
unc
tionsi
n:

-i
nit
iat
ionoft
rans
cri
pti
onandt
heb
ind
ingofRNAp
oly
mer
ase

-l
ocat
ed-20t
o-30b
asesf
romt
hes
tar
tpoi
ntoft
rans
cri
pti
on

b
)CAATb
ox-s
equenc
e-80b
pup
str
eamf
romt
hes
tar
toft
rans
cri
pti
on

-functi
ons:s
equenc
ebi
ndsr
egul
ator
ypr
otei
nst
hatmod
ifyt
her
ateoft
rans
cri
pt
ini
tiat
ion

c
)fur
therup
str
eam(
ord
owns
tream)(
1000’
sofb
p)t
her
ear
eDNAs
equenc
es

-enhancer
s-aDNAsequenc
et hatcans
timul
atetranscr
ipt
ionatan
appreci
abl
edis
tanc
ef romthesit
ewhereiti
sloc
at ed
.

-c
ont
ainsDNAs
equenc
eswhi
chb
indr
egul
ator
ypr
otei
ns

-coac t
ivator
s-"ad
apt
er"mol
ecul
esthati
ntegratesi
gnal
sfrom
acti
v atorsorrepr
ess
orsandbi
ndsorrel
aystobasalt
ransc
rip
tion
factors

-rep
res
sor
s-bi
ndtos
elect
edsetsofgenesats
itesknownass
il
enc
ers
,
whic
hsl
owtherat
eoftransc
rip
tion

1.RNApol
ymer
aseb
ind
stoas
pec
ifi
cregi
onofDNAc
all
edt
hep
romot
erwi
tht
heai
doft
rans
cri
pti
on
fact
ors

-p
romot
er-r
egi
onoft
hegenet
hats
ignal
sRNAp
oly
mer
aseb
ind
ingandt
hei
nit
iat
ionoft
rans
cri
pti
on

-tr
ansc r
ipti
onfac
tors-acc
essor
yprotei
nsnotpar
tofRNAp
oly
mer
aset
hatar
erequi
red
toini
tiateandr
egulat
et hepr
ocessoftrans
cri
pti
on

2.onl
yoneoft
he2DNAnuc
leot
idec
hai
nsc
ont
ainst
hec
orr
ectp
romot
ers
equenc
eandac
tsast
he
templ
ate
-p
romot
erl
engt
hisd
eter
minedb
yat
echni
quec
all
edDNAf
oot
pri
nti
ng

3.RNAp
oly
mer
aseb
ind
sthef
irs
tRNAnuc
leot
ide(
creat
est
he5’
endoft
het
rans
cri
pt)

I
I.El
ongat
ion:

-t
hisi
sap
oly
mer
izat
ionr
eac
tion

-d
uri
ngel
ongat
ion,RNAp
oly
mer
ase:

1.b
ind
sanuc
leos
idet
rip
hos
phat
eandmat
chesi
ttot
het
emp
lat
e

2.s
pli
tst
wop
hos
phat
egr
oup
sfr
omt
henuc
leos
idet
rip
hos
phat
eandf
ormst
hep
hos
phod
ies
terl
inkage

3.mov
est
othenextt
emp
lat
ebas
e

-d
uri
ngel
ongat
ion,s
omeoft
hei
nit
iat
ionf
act
orsar
erep
lac
edb
yel
ongat
ionf
act
ors

-RNAp ol
ymeraseli
keDNApoly
meras
ehasaproofr
eadfunct
ionandus
es
a3’ 5’exonuc
leaseac
tiv
itytor
emovei
ncor
rectorbasemisp
air
sduri
ng
trans
cr i
pti
on

I
II.Ter
minat
ion:

1.t
her
ear
esp
eci
fict
ermi
nat
ionDNAs
equenc
es,whi
chs
ignalt
heendoft
rans
cri
pti
on

2.ter
minati
onfac
tors
-functi
oninrel
eas
ingRNApoly
mer as
eandel
ongat
ionf
act
orsf
romt
heDNA
templ
ateandal
sorel
easethetrans
cri
ptfromthet
emp l
ate

3Ty
pesofRNAp
oly
mer
ases
:

1.RNAp
oly
mer
aseI-t
rans
cri
besr
RNA

2.RNAp
oly
mer
aseI
I-t
rans
cri
besmRNA

3.RNAp
oly
mer
aseI
II-t
rans
cri
bes5Sr
RNA,t
RNA,ands
nRNA’
s

St
ruc
tur
eandPr
oces
singofmRNA:

1.mRNAt
rans
cri
pti
oni
sthef
irs
tst
epi
nthes
equenc
eofev
ent
slead
ingt
opr
otei
nsy
nthes
is

2.mRNAi
str
ans
cri
bedf
romt
heDNAt
emp
lat
easap
rec
urs
ormol
ecul
ecal
ledp
re-mRNAorhnRNA

3.St
ruc
tur
eofanmRNAmol
ecul
e:

a.5’
cap
-cons
ist
sof3nuc
leot
ideswher
ethef
irs
tisani
nver
tedorr
ever
sedguani
sinenuc
leot
ide

-c
api
sad
dedi
mmed
iat
elyaf
tert
rans
cri
pti
on

-3f
unc
tionsoft
hec
ap:
 1.ai
dsi
nthei
nit
iat
ionoft
rans
lat
ion

2.ac
tsasas
ignal
,whi
chi
srec
ogni
zedb
ythenuc
learenv
elop
e

3.p
rot
ect
stheRNAf
romd
egr
adi
ngenzy
mesc
all
ednuc
leas
es

b.5’
untrans
lat
edregi
on(
5’UTR)-DNAs
equencethati
st r
ansc
rib
edi
ntoRNAb
utt
he
RNAsequenc
eisnottr
ans
latedi
ntoanaminoaci
dsequence

-f
unc
tionsoft
he5’
UTR:

1. c
ani
ncr
eas
eori
nhi
bitt
rans
lat
ionofRNAmol
ecul
e

2.containssequenceswhi
charerec
ognizedb
yr i
bosomesandac
ces
sor
ypr
otei
ns
forini
tiati
onoft ransl
ati
on-c
all
edcons
ensussequences

c
.cod
ingsequenc
es-anRNAs
equencethatbegi
nswit
hAUGi
nit
iat
orc
odon Metand
t
ermi
nateswithter
minat
orc
odonsUAG,UGA,orUAA.

-al
soc
all
edt
rans
cri
beds
equenc
est
heyar
ecomp
osedofexonsandi
ntr
ons

-exon-i
sas egmentwithinagenethatcar
riesp
artofthecodi
ng
inf
ormationforaprotein(DNAsequenc
esthatareev
entual
lytrans
lat
ed
int
oaminoac idr
esid
ues )

-int
ron-isaregi
onofagene,whi c
histranscri
bedint
oaRNAt rans
cri
pt
thatisremovedbutnottransl
ated
,byspli
cing(DNAsequenc
eswhic
hare
noteventual
lytr
anslatedint
oaminoac
idr esi
dues)

-i
ntr
onsar
eal
soc
all
edi
nter
veni
ngs
equenc
es

-spl
ic
ing-istheexcis
ionofas egmentofRNAf ol
lowedb
yarejoi
ningof
theremainingfragments(exons)whi
chiscat
alyzedbyDNAorRNAligas
e

d
.3’untr
ansl
atedr
egion(3’
UTR)-RNAsequencewhic
hf ol
lowst
hecod
ings
equenc
eand
c
ons
istsofRNAmolec
ulesthatarenott
ransl
atedintoaminoac
ids

1.3’
UTRc
ont
ainsas
hor
tAAUAAAt
hats
ignal
stheendoft
rans
cri
pti
on

-proc
essi
ngsi
gnal
-fi
xeslengt
hof3’UTRandi
ndi
cat
es
thesit
eforat
tachmentofthepol
y(A)t
ail

-pol
y(A)t ai
l-unb r
okenstri
ngofadeni
nenucleoti
des(
30-
200)addedt ot he3’endoftheRNAmolecul
eb yan
enzymep oly
( A)polymer
ase(mayfunct
ioninstabi
li
tyand
aidi
nt ranslation??)

2.3’
UTRs
equenc
esp
rov
ides
tab
ili
tyf
ort
heRNAmol
ecul
e

Pr
oces
singPr
e-mRNA’
s:

-oc
cur
sint
henuc
leus
1.ad
dit
ionof5’
cap(
whi
let
rans
cri
pti
oni
soc
cur
ring)and3’
pol
ymer
ase(
A)t
ail(
aft
ert
rans
cri
pti
on)

2.r
emov
alofi
ntr
onsb
ysp
lic
ing

a)
occ
ursbyi
nter
act
ionsofthehnRNAwithas
pli
ceos
ome-anuc
learc
omp
lexc
omp
osedof
RNA(i
nthef
ormofsnRNA)andprotei
ns

-s
tep
s:

1)
spl
ic
eos
omeb
ind
stot
hei
ntr
on

2)i
nducesaconf
ormati
onal
changeint
hei
ntronwher
ethei
nter
veni
ng
sequencef
ormsalari
atorbranc
hedRNAs
tructur
e

3)
int
roni
sremov
edandt
het
wonei
ghb
ori
ngexonsar
ejoi
ned(
byRNAl
igas
e)

-t
her
ear
econs
ens
us-s
pli
cings
equenc
esatt
heb
ound
ari
esoft
hei
ntr
on

-5’GUs equenc
eanda3’
AGs
equenc
e c
all
edaGU/
AGb
ound
ary
sequenc
e

-Ri
bos
omalRNA(
rRNA)
-mos
tab
und
antRNAf
oundi
nthec
ell

-i
dent
ifi
edi
nSued
ber
guni
tswhi
chi
sexp
res
sedi
nthes
edi
ment
ati
onc
ons
t S)1S=10-13s
ant( ec

-t
hesedi
ment
ati
onconst
antispr
oportional
totherateofsed
iment
ation(mi
grati
on)of
amol
ecul
einagi
vencent
rif
ugalfi
eldandisrel
atedtother
ingandshapeofthemolec
ule

-thefast
ert
hemol
ecul
edes
cend
sthel
argert
heSnumb
erandi
ngener
al,t
hehi
ghert
hemol
ecul
ar
weight

-eukaryoticr
ibosomes
-comp
osedof2s
ubuni
tseac
hsub
uni
tcons
ist
sofoneormor
eRNAs
pec
iesand30-
40diff
er entprot
eins

4t
ypesofr
RNA:

a)
18Sr
RNAi
sas
soc
iat
edwi
tht
hes
mal
lers
ubuni
t

b
)28S,5.
8S,and5Sr
RNAi
sas
soc
iat
edwi
tht
hel
argers
ubuni
t

-28S,18S,and5.
8Sr
RNAar
etr
ans
cri
bedasap
rec
urs
orRNAmol
ecul
ebyRNAp
oly
mer
aseI

-Lookatp
rer
RNAgenes
chemat
ic

-i
ntr
ageni
csp
acerv
s.I
ntr
ons

-5Sr
RNAi
str
ans
cri
beds
epar
atel
yasahnr
RNAmol
ecul
ebyRNAp
oly
mer
aseI
II—p
re5Sr
RNA

Lar
gep
re-r
RNAgenes(
Str
uct
ureofr
RNA’
s):

1.geneenc
odi
ngl
argep
re-r
RNA’
soc
cur
sinmul
ti
plec
opi
esi
nal
leukar
yot
es
-c
onc
ent
rat
edi
ncl
ust
ersoneukar
yot
icc
hromos
omes

-i
ncont
ras
ttomRNAgenes
,whi
choc
curl
argel
yins
ingl
ecop
ies

-eachrep
eatinthelar
gepre-r
RNAgeneclustercons
ist
sofac
odi
ngs
egmentandal
ong
int
ergeni
cspacer(
regiont
hatisnott
rans
c r
ibed)

-i
nter
geni
csp
acer
scont
ains
equenc
eswhi
chs
ignali
nit
iat
ionandt
ermi
nat
ionoft
rans
cri
pti
on

2.eac
hgenewi
thi
nthec
lus
terc
ont
ainsonec
opyof18S,5.
8S,and28Sr
RNAc
odi
ngs
equenc
es

-c
odi
ngs equenc
essep
aratedbyint
rageni
cspacer
s(s
equenc
eswhi
char
etr
ans
cri
bedb
ut
ar
elaterremovedd
uringp
r e-r
RNAp r
ocess
ing)

-2p
rimar
ypr
omot
ers
equenc
es:

1.c
orep
romot
erel
ement-30t
o+15

2.up
str
eamp
romot
erel
ement-150t
o-50

-noTATAorCAATb
oxes

-orderofsequenc es5’ 3’ are:enhancerp romotert ransc

ribedintrageni
cspacer
18Sc od
ingsequenc e transcribedint
ragenicspacer 5.8Scodi
ngs equence
transcri
bedintragenicspacer 28Sc odingsequence(exonsandintrons)i nt
ergeni
c
spacer(nottransc r
ibed
)c ontainsterminatorsequenc
es

Tr
ans
cri
pti
onandPr
oces
singofPr
e-r
RNA:

1.b
ind
ingofRNAp
oly
mer
aseIt
o5’
flanki
ngp
romot
er(
need
str
ans
cri
pti
onf
act
ors
)

-SL1t
rans
cri
pti
onf
act
or-b
ind
swi
thp
oly
mer
aseIt
othep
romot
er-c
ont
ainsTATAb
ind
ingp
rot
ein

-up
str
eamb
ind
ingf
act
or-UBF-b
ind
stoc
oreandup
str
eamp
romot
erel
ement
s

-s
timul
atesb
ind
ingofb
othSL1andRNAp
oly
mer
aseIt
othep
romot
er

2.t
rans
cri
pti
onc
ont
inuest
hrought
hel
argep
re-r
RNAgene

-c
opi
esb
othc
odi
ngs
equenc
esands
pac
erswi
thouti
nter
rup
tion

3.t
rans
cri
pti
ons
top
sati
nter
geni
csp
acer(
ter
minat
ors
ignal
s)

4.RNAp
roc
ess
ingf
oll
owst
rans
cri
pti
on

-p
re-r
RNAi
scutt
o18S,5.
8S,and28Sr
RNAmol
ecul
es

-f
irs
tst
epl
iber
ates18S+5.
8Sj
oinedt
o28S=>t
hen5.
8Sand28Sar
esep
arat
ed

-r
eac
tionst
houghtt
obec
atal
yzedb
yRNAexonuc
leas
esandend
onuc
leas
es
 
5.s
omep
re-r
RNAc
ont
aini
ntr
onswhi
chmus
tber
emov
edb
ysp
lic
ing

-notwel
lund
ers
toodb
uti
tist
houghtt
oinv
olv
esec
ond
arys
truc
tur
esofRNAmol
ecul
es

-s
elf
-sp
lic
ingofRNA(
rib
ozy
mes
)

-groupIi
ntr
onr emoval(Tetr
ahymena)
-depend
sonthepat
ter
nofs
econd
arys
truc
tur
es
setupbyi
nvert
eds equencesint
heTetrahy
menaint
ron

-groupIIi
ntronremoval(
mitoc
hond
riaandchlor
opl
ast
s)-f
ormsani
nter
med
iat
elar
iat
str
uc t
uresi
milartoremov
alofmRNAintrons

5Sr
RNA:

-geneenc
odi
ng5Spr
e-r
RNAal
sooc
cur
sinc
lus
ter
ed,mul
ti
plec
opi
es(
Why
?Thec
ell
need
s
alotofri
bos
omes
)

-eac
hgenec
ont
ainsa120b
pcod
ings
equenc
esep
arat
edb
yanont
rans
cri
bedi
nter
geni
csp
acer

-p
romot
erwi
thi
nthet
rans
cri
bedgenec
ont
ains2c
ons
ens
uss
equenc
es

-genet
rans
cri
bedb
yRNAp
oly
mer
aseI
II

Tr
ans
ferRNA(
tRNA)
:

-s
mal
lmol
ecul
es75-95nuc
leot
ideswi
thad
ist
inc
t"c
lov
erl
eaf
"st
ruc
tur
e

-ac
cep
tors
tem-f
unc
tionsi
ntheb
ind
ingoft
heami
noac
idt
othet
RNA

-mod
ifi
edb
ases
:

1.i
nfl
uenc
ethef
idel
it
yofc
odon-ant
icod
onp
air
ing

2.ens
uresb
asesr
eadt
hreeatat
ime

-ac
tual3-Ds
truc
tur
ebyx-r
ayd
iff
rac
tions
howst
RNAmol
ecul
eisl
-shap
ed

t
RNAgenes
:

-oc
curi
ncl
ust
ered
,mul
ti
plec
opi
es

-eac
hgenei
nac
lus
terc
ons
ist
sof:

1.as
hor
ttr
ans
cri
beds
pac
er(
3-10b
ases
)

2.c
odi
ngs
equenc
e

3.3’
trans
cri
beds
pac
er
-c
opi
esofgeness
epar
atedb
ynont
rans
cri
bedi
nter
geni
csp
acer

*-p
romot
eri
swi
thi
nthet
rans
cri
bedgeneandi
ssp
liti
nto2b
loc
ks:AandB

-t
rans
cri
bedb
yRNAp
oly
mer
aseI
II

-s
omet
RNAgenesc
ont
aini
ntr
ons

-i
mmed
iat
elyf
oll
owi
ngt
he3’
sid
eoft
hes
equenc
ecor
res
pond
ingt
otheant
icod
on

Tr
ans
cri
pti
onandPr
oces
singoft
RNA’
s:

-c
leav
ageof5’
spac
erc
atal
yzedb
yRNas
eP(
RNAend
onuc
leas
e)

-RNas
ePc
ont
ainss
omes
nRNA+p
rot
einsb
othofwhi
char
erequi
red

-add
iti
onoftheCCAsequencewhi
chi
sad
dedb
ytRNAnuc
leot
idy
ltr
ans
fer
ase-us
esCTP
andATPasanenergysourc
e

-i
ntr
onsr
emov
edb
yanRNAend
onuc
leas
e

-r
ecogni
zesexonb
ound
ari
es

-exonend
sar
ejoi
nedb
yRNAl
igas
e

Thust
her
ear
e3d
ist
inc
tsp
lic
ingp
athway
s:

1.intr
onremovalf
rompre-mRNAd
epend
sonr
ecogni
tionofc
ons
ens
uss
equenc
esati
ntr
onb
ound
ari
es
(part
ici
pat
ionofsnRNA’
s)

2.r
emov
alofi
ntr
onsf
romp
re-r
RNAd
epend
sonr
ecogni
tionof2os
truc
tur
eint
hei
ntr
on

3.i
ntr
onr emovalfrompre-tRNA’
sr ec
ogni
tionoft
hei
ntr
onandl
ocat
ionoft
hes
pli
cingr
eac
tionsd
epend
pri
mari
lyonregionsfor
mi ngtheexons

Smal
lnuc
learRNA’
s(s
nRNA’
s):

-Us
nRNA-p
art
ici
pat
esi
npr
e-mRNAandr
RNAp
roc
ess
ingands
pli
cing(
uri
dinei
saf
requentb
ase)

-M1s
nRNA-f
ormsp
artoft
heRNas
ePc
omp
lexwhi
chp
roc
ess
esp
re-t
RNA

Smal
lcy
top
las
micRNA’
s(s
cRNA’
s):

-f
ormp
artoft
hes
ignalr
ecogni
tionp
art
icl
e

-thi
sribonuc
leoprotei
ncompl
expar
t i
cipat
esinthereact
ionattac
hingr
ibos
omest
othe
endopl
asmicreti
culumduri
ngthesynthesi
sofsecret
oryprot
eins

s
nRNA’
sands
cRNA’
s:

-t
rans
cri
bedb
yRNAp
oly
mer
aseI
I(s
n)andI
II(
sc)
-Us
nRNA’
sjoi
nedt
osev
eralp
oly
pep
tid
est
ofor
mri
bonuc
leop
rot
eins=s
nRNP’
sors
nur
ps

-s
cRNA’
sjoi
nedt
opol
ypep
tid
esc
all
eds
cyr
ps

-codon-atri
pletofad j
acentb asesinapoly
nucleot
idec
hai
nofamRNAmolec
ulethat
codesforaspec i
ficaminoacids;thebasi
cunitofgenet
icc
odes
pec
ify
inganaminoaci
d
forincorp
orationintoap ol
ypeptidechai
n

-anti
codon-asequenc
eof3nuc
leot
idesi
nat
RNAmol
ecul
ethati
scomp
lement
aryt
othe
codontr
ipleti
nmRNA

Tr
ans
lat
ion:

-t
heas
semb
lyc
hai
nswi
thmRNAs
erv
ingast
het
emp
lat
e,ap
roc
esst
hatoc
cur
satt
her
ibos
omes

FourPhas
esofTr
ans
lat
ion:

1.Char
ging(
Act
ivat
ion)r
eac
tion

-ami
noac
idi
sjoi
nedt
oat
RNAmol
ecul
ethr
oughahi
ghener
gyb
ond

2.I
nit
iat
ion

-proc
esswherethelargeandsmallri
bosomalsub
uni
tsass
emblewi
thamRNAmol
ecul
e
andas p
eci
ali
zedchargedaminoac
y l
-tRNAcall
edani
nit
iatort
RNA

-p
roc
essc
atal
yzedb
yas
eri
esofp
rot
einsc
all
edi
nit
iat
ionf
act
ors

3.El
ongat
ion

-proc
esswher
et heami noacyl-tRNAcomp lexbind
stother
ibos
omeinsequenceaccor
ding
tothemRNAcode.Ast hes equent i
alpai
ringproceed
s,ami
noacid
saretransf
erredfro
tRNA’si
ntoagradual
lyl engtheningpoly
pep ti
dechai
n

-c
atal
yzedb
yas
eri
esofp
rot
einsc
all
edel
ongat
ionf
act
ors

4.Ter
minat
ion

-p
roc
esswher
emRNAandt
hec
omp
let
edp
oly
pep
tid
ear
erel
eas
edandt
her
ibos
omal
sub
uni
tss
epar
ate

-p
roc
essc
atal
yzedb
yas
eri
esofp
rot
einsc
all
edt
ermi
nat
ionf
act
ors

*Al
lfourp
has
esr
equi
reener
gyi
nthef
orofATPorGTP

Char
gingReac
tion(
AAAc
tiv
ati
on)
:

-act
ivat
iontakesp
lac
ein2s
tep
s(b
oths
tep
scat
aly
zedb
ythes
ameenzy
meanami
noac
yl-t
RNA
synt
hetase)

a.AA+ATP AA-AMP(
alp
ha)+PiPi(
bet
aandgamma)
 -c
all
edami
noac
yl-ad
eny
lat
ecomp
lex

b
.AA-AMP+t
RNA AA-t
RNA+AMP

-hi
ghener
gymol
ecul
e(5000-7000c
al/
mol
)

-p
rov
idest
heener
gyt
ofor
mpep
tid
eli
nkaged
uri
ngp
oly
pep
tid
elengt
heni
ng

-aaisl
inkedtot
RNAb yacoval
entbondt
othet
ermi
nalad
eni
neoft
heCCAatt
he3’
end
oftheaccept
orstemoftRNAmolec
ule

-t
her
ear
e20d
iff
erentami
noac
yl-t
RNAs
ynt
het
asesonef
oreac
hoft
he20ami
noac
ids

-NOTE:t
heami
noac
idi
tsel
fdoesnotr
ecogni
zet
hemRNAc
ode,onl
ytheant
icod
onoft
het
RNA

St
udyb
yLi
pman(
1963)
:

-c
yst
einej
oinedt
ocy
stei
ne-t
RNAb
ythep
rop
ers
ynt
het
ase

-c
yst
eine-t
RNAwast
reat
edwi
thH2andNi

-SHgr
oupc
hangedt
oH(
Cys Al
a)

-t
husCy
s-t
RNAwasc
hangedwi
thAl
a

-t
hiscomplexadd
edtoates
ttube(
inv
itr
o)s
yst
emt
hatwoul
dsy
nthes
izeHb
,res
ult
ing
Hbcontai
nedAlainp
lac
eofCys

-c
odehadb
eenf
ool
edi
ntoi
nser
tingt
hewr
ongami
noac
id

I
.Ini
tiat
ion(
5st
eps
)

a)r
ibos
omes
epar
atesi
ntol
argeands
mal
lsub
uni
ts

b
)Met
-tRNAi+GTP Met
-tRNAi-GTPc
omp
lex

-Met
-tRNAii
suni
ques
inc
eitwi
llas
soc
iat
ewi
tht
hePb
ind
ings
iteont
her
ibos
ome

c
)Met
-tRNAi-GTPas
soc
iat
eswi
tht
hes
mal
lsub
uni
toft
her
ibos
ome

d
)mRNAi
sad
ded(
requi
resener
gyi
nthef
ormofATP)

-al
soat
tac
hesus
ingt
he5’
capwhi
chal
soi
nvol
vesani
nit
iat
ionf
act
or

-s
mal
lsub
uni
twi
lls
cand
owns
treamf
romt
hec
apf
ort
hef
irs
tAUGc
odon

e)ad
dit
ionoft
hel
arger
ibos
omals
ubuni
t(r
equi
resener
gyi
nthef
ormofGTP)

-c
omp
let
edr
ibos
omewi
thmRNAandMet
-tRNAiat
tac
hedi
snowr
ead
yel
ongat
ion

I
I.El
ongat
ion(
5st
eps
)
-Pr
oces
swher
eami
noac
idsad
doneatat
imet
oagr
owi
ngp
oly
pep
tid
echai
n

-St
udyb
yDi
ntzi
s(1963)
:

-El
ongat
ionp
roc
eed
sfr
omNH2 COOHd
irec
tion

-Lab
eledRBCwi
th3H-Leu

-Ami
noac
ids
equenc
esofHbi
ntheRBC’
swasal
read
yknown

-Samp
leswer
etakenatd
iff
erentt
imesb
etween4and60mi
n

-I
sol
atedHb s
epar
atedp
oly
pep
tid
echai
n(al
phaandb
eta)

-Cl
eav
edendc
hai
nint
ofr
agment
s(us
edt
ryp
sin)

-Sep
arat
edf
ragmentb
ypap
erc
hromat
ogr
aphy

-At4mi
nonl
yCf
ragmentc
ont
ained3H

-At30mi
nChal
ffr
agmentwasl
abel
ed

-At60mi
nal
lfr
agmentwasl
abel
ed

1.Ami
noac
yl-t
RNAl
inkst
oGTP(
cat
aly
zedb
yanel
ongat
ionf
act
or)

2.Ami
noac
yl-t
RNAb
ind
stot
her
ibos
omeatt
heAs
ite

-As
ite-b
ind
sami
noac
yl-t
RNA(
tRNA’
swi
thas
ingl
eli
nkedami
noac
id)

-Ps
ite-b
ind
stRNA’
sli
nkedt
oap
oly
pep
tid
echai
n(p
ept
idy
l-t
RNA’
s)

-Dur
ingi
nit
iat
ion,t
hei
nit
iat
ort
RNAat
tac
hest
othePs
ite,ev
ent
houghi
tcar
riesonl
ya
si
ngl
eaminoaci
d

a)El
ongat
ionf
act
orandGTPb
indt
ori
bos
omewi
tht
heami
noac
yl-t
RNA

b)Aminoac
yl-tRNAbi
ndi
ngdep
end sonacor
rectc
odon:
anti
codonpairwit
hmRNAposi
tionedatAsi
te

c
)GTP GDP+Pi

d
)El
ongat
ionf
act
orandGDPr
eleas
ed

e)Energyrel
easedbyGTPhy
drol
ysi
scont
rib
utest
othe
bi
ndingofaminoacy
l-t
RNAattheAsit
e

3.For
mat
ionofp
ept
ideb
ondb
etweenami
noac
idsatAandPs
ite

a.Cat
aly
zedb
ypep
tid
ylt
rans
fer
ase(
lar
ger
ibos
omal
sub
uni
t)
 a. MetatPs itel
inkstoaminoac i
datAs i
te
b. Energyrequir
edb yMet-tRNAc omp l
exderiv
edfromt hechargi
ng
reacti
on
c. Bothaminoacidsofdipep
tidear eattachedtotRNAatt heAs i
te
d.t RNAatt heAs it
eisconvertedf r
omanami noacyl
-tRNAi nt
oap ep
tid
yl-
tRNA
e. "Empty"tRNAr emai
nsatt hePs ite

4.a)emp
tyt
RNAi
nPs
itei
srel
eas
ed

b
)Pep
tid
yl-t
RNAmov
esf
romAt
oPs
ite

-Requi
resGTPhy
drol
ysi
sandi
scat
aly
zedb
yel
ongat
ionf
act
or

5.Ri
bos
omemov
esal
ongt
hemRNAt
hroughad
ist
anc
eequi
val
entt
oonec
odon

-Thi
smov
ementi
scal
ledt
rans
loc
ati
on

-Carr
iest
hec od
onf or
merl
yattheAsi
te,wi
thi
tat
tac
hedp
ept
idy
l-
tRNA,tothePsiteandexp
osesanewc
odonatt
heAsi
te

-Tr
ans
loc
ati
onr
equi
resGTPhy
drol
ysi
s

-3el
ongat
ionf
act
orsar
einv
olv
edi
nel
ongat
ion

-Theyactasenzy
mesd o,b
ind
ingtor eac
tingmol
ecul
ess
peed
ingthei
r
int
eract
ion,andrel
eas
ingunchangedattheendofther
eact
ion

-Severalr
ibos
omesmayb
eengagedi
nel
ongat
ionf
oragi
venmRNAmol
ecul
emRNA+
attachedri
bosomes=

I
II.Ter
minat
ion:

1.Pr
otei
nsy
nthes
iss
tepwhenAs
iteofr
ibos
omeenc
ount
ersoneoft
hreet
ermi
nat
orc
odons

-Pol
ypep
tid
eisr
eleas
edf
romt
her
ibos
ome

-Emp
tyt
RNAatt
hePs
itei
sej
ect
ed

-Ri
bos
omals
ubuni
tss
epar
atef
romt
hemRNA

-Thes
ereac
tionsar
ecat
aly
zedb
yas
ingl
eter
minat
ionf
act
or RForr
eleas
efac
tor

2.Ter
minat
orc
odonc
aus
esRFandGTPt
obi
ndatAs
itei
nst
eadofami
noac
yl-t
RNA

3.RFbi
ndings
timul
ateshy
drol
ysi
soft
heb
ondhol
dingt
hep
oly
pep
tid
echai
ntot
het
RNAatt
hePs
ite
(GTP GDP+P)

4.Si
ncenonewami
noac
idi
sloc
atedatt
heAs
ite,hy
drol
ysi
sfr
eest
hep
oly
pep
tid
echai
n

 
 

Diff
usion:i
sthemov
ementofmolec
ulesacr
ossaconc
ent
rat
iongr
adi
entf
romt
hear
eaofhi
gher
concentrat
iont
othear
eaoflowerconcent
rati
on.

Osmosi
s:thepassageofas
olv
ent(
wat
er)t
hroughamemb
ranef
romad
ilut
esol
uti
oni
ntoamor
e
conc
entratedone.

Osmoti
cpres
sure:i
stheforc
eres
ult
ingf
romd
iff
erenc
esi
nsol
utec
onc
ent
rat
ionsonop
pos
ites
idesofa
semi
permeabl
emembrane.

Sol
ute-i
sthes
ubs
tanc
edi
ssol
vedi
nas
olut
ion.

Sol
vent
-ist
hes
ubs
tanc
eus
edf
ord
iss
olv
inganot
hers
ubs
tanc
e.

Sol
utec
onc
ent
rat
ion-i
sthet
otalnumb
erofd
iss
olv
edp
art
icl
esf
oruni
tvol
umeofs
olut
ion.

Des
cri
pti
onsofr
elat
ives
olut
econc
ent
rat
ions
:

Hy
per
toni
c-i
sas
olut
ionwhos
eos
mot
icp
res
sur
eisgr
eat
ert
hant
hatofas
tand
ards
olut
ion.

Hy
pot
oni
c-i
sas
olut
ionwhos
eos
mot
icp
res
sur
eisl
esst
hant
hatofas
tand
ard1.

I
sot
oni
c-isasolut
ionwhos
eos mot
icp
res
sur
eisequalt
othatofas
tand
ardoneex:s
alts
olut
ionhas
s
ameosmoti
cpressur
easblood

Pl
asmol
ysi
s-i
sthes
hri
nki
ngoft
hep
rot
opl
asmofac
elld
uet
othel
ossofwat
erb
yos
mos
is.

Pas
siv
et ransp
ort(di
ffus
ion)
-as
sis
tedmov
ementofmol
ecul
esf
romar
easofhi
ghc
onc
ent
rat
iont
oar
eas
ofl
owc oncent
rati
on.

Rat
eofd
iff
usi
ond
epend
son:

1.Sol
ubi
li
tyoft
hep
ermeant(
inmemb
ranes
,hy
drop
hob
icmol
ecul
esd
iff
usef
ast
er)

2.Mol
ecul
ars
truc
tur
eoft
hep
ermeant
.

3.Mol
ecul
ars
izeoft
hep
ermeant

Faci
litatedd i
ffusion-i
sthemovementofmolecul
esfr
omaregi
onofhi
ghconcentrati
ontooneofl
ow
concent r
ationt hatoccur
smorerapid
lythanitwoul
dthr
oughtheb
asi
cconcentr
at i
ongr
adient
;atan
enhanc edrate.

Act
ivetrans
por
t-themovementofmater
ialsac
rosscel
lmembranesf
romregionsoflowerc
onc
ent
rat
ion
toregi
onsofhi
gherconc
entrati
on,r
equi
ringtheexp
end i
tur
eofmetabol
icenergy.

Fl
uidmos
aicmod
el:
-Pr
opos
edi
n1972b
ySi
ngerandNi
chol
son

-Isthecurrent
lyacceptedmodel ofthestruc
tureofthec yt
oplasmicmemb r
anet hat
descri
besthi
smembraneasal i
pidbi-l
ayerofprotei
nsdist
ribut
edi namos ai
c-l
ike
patternonthesurf
ac eandinthei nteri
orofthememb r
ane,wit hlater
alaswellas
transver
semovementofp rotei
nsoc curri
ngthroughthestruct
ur e.

-Lipi
db i
-layeri
samp hi
pathi
c-mol
ecul
ehav
ingofhy
drop
hob
icandhy
drop
hil
icr
egi
ons
(dualsol
ub i
li
typrop
er t
ies
)

-Hydrop
hob
icregi
ons,conc
entrat
edi
nt hemembraneint
eri
or,creat
eab
arr
iert
hat
prev
entsfreemovementofpol
armol
eculesac
ros
st hemembrane.

-Hy
drop
hil
icr
egi
onsf
acet
hewat
ery
-pol
ars
urf
aceoft
hememb
rane

-Inaddi
tiont
op rotei
nsandlip
ids,carbohy
drat
esar
eal
sop
res
enti
ncel
lmemb
ranesi
n
thefor
mofgl yc
op r
oteinsandgly
c ol
ipi
ds.

Li
pid
s(i
nmemb
rane)
:

1.Phos
phogl
ycer
ides
:

-Mos
tab
und
antl
ipi
dinmemb
ranes

-Comp
osedoft
wof
att
yac
idsc
hai
ns,ap
hos
phat
egr
oup
,andanal
cohol
orgl
ycer
olgr
oup

-Amp
hip
athi
c(p
olarandnonp
olargr
oup
s)

2.Sp
hingol
ipi
ds(
gly
col
ipi
ds)
:

-Li
pidwi
that
tac
hedc
arb
ohy
drat
esgr
oup
s

-Bac
kbones
truc
tur
eisc
all
edas
phi
ngos
inewhi
chi
sas
eri
neat
tac
hedt
oaf
att
yac
id

-NH2gr
oupofs
eri
neat
tac
hest
oas
econdf
att
yac
idc
hai
n-OHgr
oupofs
eri
ne

-I
fOHgr
oupi
sunb
oundi
tisc
all
edac
erami
de

-OHgroupcanattac
htoap hos
phate-al
coholmolec
ulei
scal
ledas
phi
ngomy
eli
n(2f
att
y
aci
dchains+ser
ine+phos
phategroup+c hol
ine)

-OHgr
oupc
anal
soat
tac
htoac
arb
ohy
drat
egr
oup
,whi
chi
scal
ledagl
ycos
phi
ngol
ipi
d

3.Gl
ycos
phi
ngol
ipi
dshav
e2f
unc
tions
:

a)Func
tioni
nmemb
ranes
tab
ili
zat
ion

b
)Al
sof
unc
tioni
nner
vec
ell
s(gangl
ios
ides
)

-Ther
ear ehumandi
seasesrel
atedtomalfunc
tioni
nthemet
abol
is
mofgl
ycer
olass
uch
asneurol
ogic
aldi
sor
ders(Tay-Sac
h'sd
isease)
4.St
erol
:

-Bas
edonf
ramewor
kof4c
arb
onr
ing

-Pr
edomi
nants
ter
oli
schol
est
erol

a)Mol
ecul
esd
ist
urbt
hec
los
epac
kingofhy
droc
arb
onc
hai
nsofmemb
ranep
hos
phol
ipi
ds

b
)Memb ranescontai
ningchol
est
erol
remai
nfl
uidatl
owt
emp
erat
uresr
athert
han
"
freezi
ng"intononfl
uidforms

c
)Chol
est
erolal
soi
ncr
eas
est
hef
lexi
bil
it
yandmec
hani
cals
tab
ili
tyofmemb
ranes

Memb
ranep
rot
eins
:

1.10-50d
iff
erentt
ypesofmemb
ranep
rot
eins
:10,
000t
o250,
000mol
ecul
arwei
ght

2.Hy
drop
hob
ic(
hyd
rop
hil
ic
)ami
noac
idsar
ecl
ust
eredt
hisf
ormsanal
phahel
ixt
hatc
ans
panamemb
rane

-Thes
etr
ans
memb
ranes
egment
sac
tasanc
hor
stohol
dthep
rot
eini
nthel
ipi
dbi
-lay
er

-Amembr
anepr
oteinc
anbecomposedofsev
eralt
rans
memb
ranes
egment
s,whi
chext
end
bac
kandfor
ththr
oughthel
ipi
dbi
-layer

-Eachs
egmentconnec
t edbyastretc
hofhyd
rop
hil
icami
noac
idst
hatar
epr
esenton
eit
hertheout
sid
eort heinsi
deofthememb
rane

-Somemembraneprot
einsmayhaverep
eat i
ngami
noac
ids
equenc
es,whi
chc
anf
orm
second
arys
tructur
es uchasanal
phaheli
x

-Ar
rangementc
anp
lac
ehy
drop
hob
icami
noac
idsonones
ideandhy
drop
hil
icami
noac
idsont
heot
her

-Cancr
eateapol
archannel(
thi
sisus
edtotrans
por
tmol
ecul
est
hrought
hememb
rane)
thes
eprot
einsar
ecall
edTransp
ortpr
otei
ns

-Membraneprot
einscanal
soc
ont
ainat
tac
hedc
arb
ohy
drat
egr
oup
sthatar
est
rai
ghtor
branc
hed(2-60units
)

-Car
bohy
drat
esar
eus
ual
lyonc
ellmemb
ranes
urf
aces

-Cel
lmemb
rane+s
urf
acegl
ycop
rot
eins=gl
ycoc
aly
x

A.Func
tionsoft
hegl
ycoc
aly
x:

1.Ad
dst
abi
li
tyt
omemb
raneb
yhy
drogenb
ond
ing

2.Ac
tasr
ecogni
tions
ites(
binds
ignal
mol
ecul
es)ofmemb
raner
ecep
tor
s

3.Cel
l-c
ell
adhes
ion

Cel
lmemb
ranef
unc
tion:
1.Si
ngerpr
oposedanal
ter
nat
ingc
onf
irmat
ionmod
elt
oexp
lai
nhowt
rans
por
tpr
otei
nsc
arr
yout
faci
li
tat
eddi
ffusi
on

A.Tr
ans
por
tpr
otei
nshi
ftsb
etween2c
onf
ormat
ionswi
thi
nthememb
rane

B.I
nit
ial
ly
,pr
otei
nsf
old
eds
otheexp
osedb
ind
ings
itei
sfac
ingt
her
egi
onofhi
gherc
onc
ent
rat
ion

-Hi
ghaf
fini
tys
tat
ebi
ndss
trongl
ytot
rans
por
tedmol
ecul
e

-Bi
ndi
ngoft
rans
por
tedmol
ecul
etob
ind
ings
iteoc
cur
svi
arand
omc
oll
is
ions

C.Bindingoftransport
edmolecul
etob ind
ingsitecaus
esaconformationalc
hangeofthe
integralmembraneproteins
otheb i
nd i
ngsit
ec ont
aini
ngthetransportedmolec
ulei
s
exposedt othesit
eoft hemembranewher etherei
salowconcentrati
onoft he
transportedmolecul
e=lowaffi
nitystate

D)Lowaf
fini
tys
tat
eal
lowst
het
rans
por
tedmol
ecul
etob
erel
eas
ed

E)Ret
urnst
hei
ntegr
almemb
ranep
rot
eint
othehi
ghaf
fini
tyc
onf
ormat
ion

Cel
lul
arp
rot
eint
rans
por
ter
s:

1.Or
gani
ctr
ans
por
ter
s-f
aci
li
tat
est
hed
iff
usi
onofs
mal
lor
gani
cmol
ecul
es(
E.X.gl
ucos
e)

2.Ani
onc
arr
ier
s-f
aci
li
tat
est
hed
iff
usi
onofnegat
ivel
ychar
gedi
nor
gani
cgr
oup
s

3.I
ont
rans
por
ter
s-(
trans
por
tss
odi
um,p
otas
sium,c
alc
ium,c
hlor
ine)

-Mostionchannel
saregat
ed(
comp
osedofp
rot
eins
)-c
ont
rol
andc
anexi
sti
nop
en,c
los
e,
orint
er medi
atestat
es

-Gat
ed-i
onc
hannel
s-c
ond
uctner
vei
mpul
ses

-Al
ltr
ans
por
terp
rot
einsar
e

1. Integralmemb raneprot
einscontai
ningsev
eral
alp
ha-heli
cal
segment
st hat
zigzagb ackandforthacros
st hemembrane
2. Glycoproteins(
plasmamemb r
ane)withcarb
ohyd
rategroupsdi
rec
tedtowardthe
cellext
er i
or

A)Gl
ucos
etr
ans
por
ter
-si
xdi
ffer
entt
ypes
:

-Cons
ist
sof
:

1.As
ingl
epr
otei
nwi
th12al
phahel
ic
als
egment
s,whi
chs
pant
hec
ell
membr
ane

2.Segment7,8,and11f
romt
rans
por
terp
ore
 -Gl
ucos
emor
econc
ent
rat
edout
sid
eofc
ell(
sev
enX.
)

-Gl
ucos
eimmed
iat
elyc
onv
ert
edt
ogl
ucos
e-6-p
hos
phat
ewheni
tisi
nthec
ytop
las
m

-Gl
ucos
e-6-p
hos
phat
ecannotp
assb
ackt
hroughmemb
rane

-Somegluc
oset
ransp
orter
sregulat
edbyhormoneins
uli
n,whi
ch
sti
mulat
esmuscl
eandfatcel
lst
oallowgl
ucosetoenter

B)Pas
siv
eionp
rot
eint
rans
por
ter
s:

-Cond
uctc
har
gedi
onss
odi
um,p
otas
siumorc
alc
iumandal
soc
hlor
inei
ons

-Mos
tonc
hannel
sar
eop
enorc
los
edb
ygat
es

-Ther
ear
ethr
eet
ypesofgat
es:

1)Volt
age-gat
edchannel-opensorcl
osesinresp
ons
e
tochangesint
hevolt
aged i
fferenc
eacrossthe
membranehousi
ngthechannel

-Sodi
um,potas
sium,c
alc
iumi
nvol
vedi
ncond
uct
ionof
nerv
eimpuls
es

2)Ligand-gatedc hannel
-op ensorc l
osesinresp
onseto
bindi
ngs pec
ifi
cc ontrolmolecules(hormones,
neurotransmitt
er s)(achlorine-l
igandchanneldef
ect
invol
vedincysticf i
brosi
s)

3)Mechanosensi
tiv
e( str
et c
h-gated )channel
-op
ensor
cl
osesinresponsetomec hanical
st r
essont hemembr
ane;
gatesoccurinmulti
ple,cl
oselyrelatedforms

E.X.:mammal
ianb
rai
ncel
lshav
ethr
eer
elat
edv
olt
age-gat
eds
odi
um
channel
s

E.X.
:>30t
ypesofp
otas
siumc
hannel
s(s
omev
olt
ages
omel
igand
)

Ac
tiv
eTr
ans
por
t:

-Subst
anc etranspor
tedact
ivel
ysod
ium,p
rot
eins
,cal
ci
um(
otheri
ons
);gl
ucos
e(s
ix
carb
ons hutt
er s)
;aminoac
ids

1)Goesagai
nstc
hemi
calorel
ect
ric
algr
adi
ent

2)Requi
resener
gyandi
ssens
iti
vet
omet
abol
icf
act
ors

3)Dep
end
sont
hep
res
enc
eoff
unc
tional
memb
ranep
rot
eins

4)Canb
esat
urat
ed

5)I
ssp
eci
fi
cforc
ert
ains
ubs
tanc
esorc
los
elyr
elat
edgr
oup
sofs
ubs
tanc
es
-Ac
tiv
eTr
ans
por
tpump
s(d
irec
tlyd
epend
entonATP)(
dir
ectac
tiv
eTr
ans
por
tpump
s):

1)P-ty
pepump-temporar
il
ybi
ndsap
hos
phat
egr
oupr
emov
edf
romATP
duri
ngthepump
ingcy
c l
e

2)V-typ
ep ump(
v=v
esi
cl
e)-p
umpb
reaksd
ownATPast
hei
rener
gys
our
cef
romac
tiv
e
trans
port

-Pump
sdonotb
ondap
hos
phat
e(f
romATP)d
uri
ngt
hei
rpump
ingac
tion

-Examp
lesar
eF0F1ATPas
einmi
toc
hond
ria

I
.P-t
ypep
ump
s:

1)Pr
otonATPas
epump
-mov
esp
rot
onsoutofc
ell(
ATPas
ecanwor
kinb
othd
irec
tions
)

2)Cal
ci
um-ATPas
epump
-pus
hesc
alc
iumoutofc
ell

-Pus
hesc
alc
iumi
ntoc
ytop
las
m

3)Sod
ium/p
otas
sium-ATPas
e-mov
est
hrees
odi
umsout
war
d;mov
esp
otas
sium2i
nwar
d

-Ac
har
gei
ssetupout
sid
ethememb
rane

I
I.Op
erat
ionofs
odi
um/p
otas
siumATPas
epump
:

1)Pumpb
ind
sandhy
drol
yzesATP

-Phos
phat
efr
omATPt
rans
fer
redt
otr
ans
por
ter(
ATPt
oADP+Pis
til
lbound
)

-Phos
phor
ylat
edp
umpi
sahi
ghener
gyc
omp
lex

2)Phos
phat
ebi
ndi
ngc
onv
ert
ssod
ium-b
ind
ings
itet
oit
shi
ghaf
fini
tys
tat
e

-Bi
ndst
hrees
odi
umsont
hec
ytop
las
mics
ideofmemb
rane

3)Sodi
umb i
ndi
ngtr
igger
s"aconfor
mat
ional
change"oft
het
rans
por
ters
othes
odi
um-b
ind
ings
itei
s
for
cingthemedi
umoutsi
dethecel
l

4)Sod
iumb
ind
ings
itec
hangesf
romahi
ghaf
fini
tySt
atet
oal
owaf
fini
tySt
atef
ors
odi
um

-Rel
eas
ess
odi
umt
omed
iumout
sid
eoft
hec
ell

5)Potassi
umbi
ndi
ngs
itei
sal
ter
edt
oahi
ghaf
fini
tys
tat
eandp
otas
siumout
sid
ethec
ell
bind
stot
he
trans
p or
ter

6)Bi
ndi
ngofpotas
s i
uminducesaconf
ormat
ional
changeoft
het
rans
por
ters
othatt
hep
otas
sium-
bi
ndi
ngsit
efacesthecy
t opl
asmi
cofthecel
l

-Remai
ningp
hos
phat
egr
oupr
eleas
edi
ntoc
ytop
las
mic
7)Pot
ass
iumr
eleasedi
ntothec
y t
oplas
mandat
rans
por
terc
onf
ormat
ional
changer
ever
tst
hep
otas
sium
-bi
ndi
ngsi
tet
oal owaffi
nit
ystate

I
II.I
ndi
rec
tac
tiv
eTr
ans
por
tpump
s(s
ugar
s,ami
noac
ids
,andi
ons
):

-Us
eani
onc
onc
ent
rat
iongr
adi
entmai
ntai
nedb
yanot
her
,di
rec
tac
tiv
etr
ans
por
t,asanener
gys
our
ce

-Cotr
anspor
t-mol
ecul
esc
ar r
iedinoroutofcel
lsb
yindir
ectact
ivet
ranspor
talway
s
movesac
rossmembr
anewithionswhi
chsuppl
ythedri
vingfor
cefortrans
port

1)2t
ypesofi
ndi
rec
tac
tiv
eTr
ans
por
t:

a)Symport-c
ot ransp
or t
edsubst
ancemovesi
nthesamedir
ecti
onasthedri
vingi
on(
E.X.
ofmolec
ulestransportedint
hisfas
hionares
ugar
s,aminoaci
ds,andi
ons
)

b
)Anti
port
-c ot
rans
portedsub
stanc
emov
esi
ntheop
pos
ited
irec
tiont
othed
ivi
ngi
ons
(
als
osugars
,aminoaci
ds,andi
ons)

-Not
e:t
her
ear
esi
zel
imi
tat
ions

I
V.Cel
lsur
fac
e:

-Cel
lsur
fac
econt
ainsgl
ycol
ipi
dsandgl
ycop
rot
eins

-Ser
vesass
iteofr
ecogni
tion

-E.X.majorsyst
emscompat
ibi
li
tycomp
lex(MHC)thegenet
icregi
oninhumanbei
ngs
thatcont
rolsti
ssuec
ompati
bil
it
yandthedevel
opmentandact
ivati
onofpartoft
he
immunerespons
e

-Pr
esent
sint
end
stot
hei
mmunes
yst
em

-E.X.bl
oodtype-animmunol
ogi
cal
lydi
sti
nct,genet
ical
lyd
eter
mineds
etofant
igens
(gl
ycop
rotei
ns)ont hesur
faceofRBC'
s(A,B,AB,andO)

1.Sur
fac
erec
ept
orsandi
ntr
acel
lul
ars
ignal
ing:

-Sur
facerec
eptorsar
emembr
ane-s
panni
nggl
ycop
rot
eins
-segment
sext
end
ingonb
oth
si
desofthecel
lmembrane

-Rec
ogni
zeandb
inds
ignalmol
ecul
esi
next
rac
ell
ularmed
ium

-Segmentonout
sid
erec
ogni
zest
hes
ignal(
pep
tid
ehor
mones
,gr
owt
hfac
tor
s,neur
otr
ans
mit
ter
s)

-Bi
ndi
ngb
yther
ecep
tor
str
igger
sac
omp
lexi
nter
nalr
esp
ons
einc
ell
rec
eiv
ingt
hes
ignal

-I
ncr
eas
eord
ecr
eas
einr
ateoft
rans
por
t

-Sec
ret
ion

-Oxi
dat
ivemet
abol
is
m
-I
nit
iat
ionofc
elld
ivi
si
on

-Cel
lmov
ement

V.Char
act
eri
sti
csofr
ecep
tor
s-r
esp
ons
esi
gnal
ingp
athway
s:

1)Signalmod
eld
oesnotp
enet
rat
eint
othec
ellt
oind
ucear
esp
ons
e(b
ind
ingt
oas
urf
acer
ecep
tor
sis
suff
icient
)

2)Nor
esp
ons
eisp
rod
ucedi
fthes
ignalmod
eli
sdi
rec
tlyi
njec
tedi
ntot
hec
ytop
las
m

3)Rec
ept
orsr
emai
nint
hec
ellmemb
rane;i
tdoesnotent
ert
hec
ell
toi
nit
iat
ether
esp
ons
e

-S.T.A.T.S.-s
ignalt
rans
duc
tionandb
lankoft
rans
duc
tion

4)Ther
ear
eal
imi
tednumb
erofi
nter
nalr
esp
ons
epat
hway
sthats
har
esev
eralc
ommonf
eat
ures

a)1s
har
edf
eat
ureofal
list
heus
eofp
rot
einki
nas
esi
nint
ernalr
esp
ons
epat
hway
s

1)
-pr
otei
nki
naseisanenzyme,whi
chat
tac
hesp
hos
phat
egr
oup
sder
ived
fr
omATPtospec
ifi
ctargetpr
otei
ns

2)-ed
iti
onofthephos
phategroupinhi
bit
sorst
imul
atestheac
tiv
ityof
thetargetp
rotei
norprot
einsincarryi
ngoutacel
lul
arr
eacti
on

-Examp
lesoft
argetp
rot
eins
:

A)Enzymesc
arr
yingoutc
rit
ical
step
sinmet
abol
ic
pathways

B)Tr
ans
por
tpr
otei
ns(
ionc
hannel
s)

C)Rep
res
ent
sal
lpr
otei
ns

D)Pr
otei
nsr
egul
ati
nggeneac
tiv
ity

E)Ot
herr
ecep
tor
s

3)-prot
einki
nas
esusual
lyfunct
ioni
nthef
inals
tep
sofar
eac
tion
sequenc
eacti
vatedb
yareceptors

-Pr
otei
nkinas
esmaybeassoc
iatedwit
hmemb r
aneor
sus
pendedi
nsolut
ioni
nthecytopl
asmornuc
leus

b
)Protei
nphos
p hatases
-enzymesthatremovep
hos
phat
egr
oup
sfr
omt
argetp
rot
eins
(
count
erbal
ancet heacti
vit
yofprotei
nkinas
es)

VI
.Rec
ept
orswi
thi
ntegr
alp
rot
einki
nas
eac
tiv
ity
:

-Examp
les
:
 1)I
nsul
in-c
ont
rol
sgl
ucos
eup
takeandmet
abol
is
mbyt
hec
ell

2)Ep
ider
malgr
owt
hfac
tor(
EGF)

3)Pl
atel
et-d
eri
vedgr
owt
hfac
tor(
PDGF)

-EGFandPDGFr
egul
atec
ellgr
owt
handd
ivi
sioni
nani
mal
s

1.St
ruc
tur
e(t
rans
memb
raner
ecep
tor
s)

-Ext
rac
ell
ular
-cont
ainsb
ind
ings
itef
ort
hes
ignal

-I
ntr
acel
lul
ar(
cyt
opl
asmi
c)-c
ont
ainsp
rot
einki
nas
esi
te

-Ext
rac
ell
ularandi
ntr
acel
lul
arc
onnec
tedb
yal
phahel
ixwhi
chs
panst
hememb
rane

2.Bindi
ngofs i
gnali
nducesconfor
mat i
onalc
hangeofi
ntrac
ell
ularrecep
tor
s,whi
chbindsphos
phate
groupstotyrosi
ne(y)resi
duesont herec
eptor
sortotyr
osineresi
duesontar
getpr
ot ei
ns(ty
rosi
ne
protei
nkinas
es )

3.Addi
tionofphos
phategroup
stothereceptor
siscal
leds
elf
-phosphor
y l
ati
onofrecep
tor
s=
autop
hos p
hory
lati
oncanleadtoac
tiv
ationofotherpr
otei
nkinasesinthecytop
las
m

4.Add
iti
onofphosphat
etot
argetp
rot
einsmayei
thers
timul
ateori
nhi
bitac
tiv
ityoft
argetp
rot
einsi
n
themetabol
icp
athway

VI
I.Examp
leofr
ecep
tor
swi
thi
ntegr
alp
rot
einki
nas
eac
tiv
ity
:

-EGFr
ecep
tor
-inv
olv
est
heRasp
rot
ein

1.Bind
ingofhormoneorsignalorgrowt
hfac
toratt
hec
ell
sur
fac
esi
nduc
esac
onf
ormat
ional
change
thatacti
vat
et heprot
einkinasesi
te

2.Phos
phat
egr
oup
sbi
ndt
orec
ept
orc
omp
lexi
ncy
top
las
m

3.Phos
phat
egr
oup
sonr
ecep
torar
erec
ogni
zedb
yanad
apt
erp
rot
ein

4.Ad
apt
er+ap
hos
phor
ylat
edr
ecep
torac
tiv
ateas
econdp
rot
ein(
guani
nenuc
leot
ider
eleas
efac
tor
-GRF)

5.Ac
tiv
atedGRFr
emov
esGDPf
romRasp
rot
ein-Rasi
nthe"
offs
tat
e"i
sboundt
oGDP

6.Rasp
rot
einb
ind
sGTPandb
ecomesac
tiv
ated"
ons
tat
e"

7.Acti
vatedRasc
anac
tiv
ateoneormor
epr
otei
nki
nas
es,whi
chl
ead
stot
hep
hos
phor
ylat
ionoft
arget
prot
eins

-I
frec
ept
ori
sboundt
oext
rac
ell
ulars
ignal
,Rass
tay
sonandt
hep
athways
tay
son.

-I
frec
ept
orb
ecomesunb
oundt
oext
rac
ell
ulars
ignal
,Rasi
stur
nedof
fandp
athways
hut
sof
f.

-Ther
eexi
stsal
ter
ed(
mut
ant
)for
msofRast
hathav
edef
ect
iveGTPas
eac
tiv
ity
;pr
otei
nisc
ont
inual
ly
on

-Pr
esenti
nmanyt
ypesofc
anc
er

I
X.Rec
ept
orswi
ths
epar
atep
rot
einki
nas
eac
tiv
ity

1.Rec
ept
orsar
ecomp
lexp
rot
einswi
ths
event
rans
memb
ranes
egment
s

2.Bi
ndi
ngandextr
acel
lul
arsi
gnalmod
ule,ter
medthe1stmes
sengeri
nthes
epat
hway
s,ac
tiv
atesan
enzy
matics
iteonthec
y t
opl
asmi
cendoft her
ecep
tors

3.Cyt
opl
asmi
csi
tecatal
yzesthefi
rstst
epinthes
eri
esofs
epar
ater
eac
tionsl
ead
ingt
otheac
tiv
ati
on
ofoneormor
eprot
einki
nasesreacti
onser
ies
:

a)Pr
imar
yreac
tions
eri
esf
oll
owi
ngac
tiv
ati
onofr
ecep
torf
oll
owsoneoft
wop
athway
s

b
)Fi
rsts
tepi
sac
tiv
ati
onofaGp
rot
ein

-Gp r
otein-oneofal ar gefamilyofhet er
otrimer
icGTP-bi
ndi
ngp rot
eins
thatareimp ort
anti ntermed i
ariesincell
-si
gnali
ngpathways.Us
uall
y
acti
vatedb ytheb i
ndingofahor moneorot hersi
gnal
ingli
gandtoa7-
passtransmemb raner ecep
t orpr ot
ein

c
)Gp
rot
einac
tiv
atesanenzy
meknownasanef
fec
tor

d
)Ef
fec
torgener
atesoneormor
e2ndmes
senger
s-s
mal
lmol
ecul
est
hatac
tiv
atep
rot
einki
nas
es

-Thesep
roteinki
nasesareac
tiv
atedb
ythead
dit
ionofPO4gr
oup
sto
seri
neorthreoni
neaminoaci
ds

Gp
rot
eins
:

-Bi
ndGTPandGDP

-Cons
istsoft
hreepoly
pepti
dec
hai
nsas
soc
iat
edwi
thc
ytop
las
mics
ideoft
hep
las
ma
membraneasaheterotr
imer

I
.Per
ipher
alp
rot
eins

1)Al
phac
hai
ncont
ainsGTP/GDPb
ind
ings
ite

-GDPb
ound
;al
phac
hai
nboundt
obet
aandgammac
hai
ns;al
phac
hai
ninac
tiv
e

-I
f"Of
f"s
tat
e,i
tisat
rimer

2)If1s
tmessengerboundtorec
ept
or,GTPbecomesb
oundt
oal
phac
hai
n(r
epl
acesGDP)
-ac
tiv
atesal
pha
chai
nthatr
eleasesf
romb et
aandgammachains

3)Al
phac
hai
nac
tiv
atesef
fec
tor

4)GTP->GDPandt
henal
phac
hai
nthens
hut
sof
f(r
eac
tiv
atedb
yanot
hermol
ecul
eofGTP)onandof
f
s
tat
es

I
I.Twomaj
or2ndmes
sengerp
athway
sthatut
il
izeGp
rot
eins
:

-Bothmajorpathwaysrecep
tor-respons
epathway
sgenerate2ndmessenger
sto
acti
vatep
r ot
einkinases(
effec
t orsandsec
ondmessenger
saredi
ffer
ent )

1)cAMP-c
ycl
icAMP-nuc
leot
idet
hati
sgener
atedf
romATPi
nres
pons
etohor
monal
sti
mul
ati
onofc
ell
sur
fac
erec
eptors

-c
AMPac
tsasas
ignal
ingmol
ecul
ebyac
tiv
ati
ngaki
nas
eiti
shy
drol
yzedt
oAMPb
yap
hos
phod
ies
ter
ase

-Ef
fec
torad
eny
lat
ecy
clas
ewi
llac
tiv
atecAMPast
hes
econdmes
senger

-I
nthi
spat
hwayhor
monesandneur
otr
ans
mit
ter
sac
tast
he1s
tmes
senger

-Pr
otei
nki
nas
esac
tiv
atedb
ycAMPar
ecal
ledp
rot
einki
nas
eA.

-Oneexamp
leofac AMPrec
ept
or-r
esp
ons
epat
hwayi
sthes
eri
esofr
eac
tionsus
eto
breakd
owngly
cogen-gl
ucos
e

2)I
nsP3/DAGp
athway
:

-Thesecondpathwaygeneratestwo2ndmes sengersgenerat
edthr
ough
thebreakdownofamemb ranephosphol
ipi
d,phosphati
dyli
nosi
tol
(cat
alyzedbytheeffec
torphosphol
ipas
ec )

-I
nos
itolt
rip
hos
phat
e(I
nsP3)

-Di
acy
lgl
ycer
ol(
DAG)

I
II.Op
erat
ion(
mec
hani
sm)ofI
nsP3/
DAGp
athway

a)Bi
ndi
ngofhor
moneorneur
otr
ans
mit
ter
sac
tiv
ater
ecep
tor
s

b
)Ac
tiv
ati
onal
lowsGTPt
obeb
oundt
other
ecep
tor

c
)Di
ssoc
iat
ionofal
phac
hai
nofGp
rot
einandb
ind
ingofal
phac
hai
ntop
hos
phol
ipas
ec

d
)Ac
tiv
ati
onofp
hos
phol
ipas
ecc
aus
est
heb
reakd
ownofp
hos
phat
idy
linos
itol
toI
nsP3andDAG

e)I
nsP3i
srel
eas
edf
romt
hec
ellmemb
raned
iff
usest
hrought
hec
ytop
las
mtot
heend
opl
asmi
cret
icul
um

-I
nsP3b
ind
stot
heI
nsP3r
ecep
tor(
li
gand
-gat
edc
alc
iumc
hannel
;Ins
P3i
sthel
igand
)

-I
nsP3b
ind
ingop
enst
hec
hannelandr
eleas
esc
alc
iumt
othec
ytop
las
m

f
)Cal
ci
umac
tsasas
upp
lement
als
econdmes
sengeri
nthep
athwayac
tiv
ati
ngp
rot
einki
nas
es

g)Theot
her2ndmes
senger
,DAG,i
sint
hep
las
mamemb
rane
 -Pr
imar
yfunc
tioni
stoac
tiv
atep
rot
einki
nas
es

-Ac
tiv
ati
ont
akesp
lac
eont
hei
nners
ideoft
hep
las
mamemb
rane

h)DAGacti
vat
esp r
ot ei
nkinases(
prot
einki
nas
eCf
ami
ly)(
C=c
alc
iumac
tiv
atedki
nas
es)
(ser
ine/
thr
eonineprotei
nkinases
)

I
V.Tar
get
sofp
rot
einki
nas
eC:

a)Chr
omos
omalp
rot
eins

b
)Tr
ans
por
tpr
otei
ns

c
)Cont
rac
til
eandc
ytos
kel
etalp
rot
eins

d
)Pr
otei
nsr
egul
ati
ngs
ecr
eti
onandend
ocy
tos
is

e)Enzy
mes
-met
abol
ic

-Ki
nas
esmayi
nhi
bitors
timul
ateamet
abol
icp
athway

-Cal
ci
ummayi
nter
actwi
thac
ont
rol
prot
einc
all
edc
almod
uli
n

-Ubiqui
touscal
cium-bind
ingprot
einwhereb
ind
ingt
oot
herp
rot
einsi
sgov
ernedb
y
changesinintr
ac el
lul
arcal
ci
umc onc
entr
ati
ons

-I
tsb
ind
ingmod
ifi
est
heac
tiv
ityofmanyt
argetenzy
mesandmemb
ranet
rans
por
tpr
otei
ns

-Cal
modul
in-rec
ogni
zesa20aminoaci
ds equenc
ethatcontai
nspos
iti
veaminoacid
s(R,K,
H)thatal
ternatewi
thhyd
rophobi
caminoac i
dswhi
chformsandamphi
pathi
calphahel
ix

Cel
lad
hes
ion:

-Cel
lat
tac
hment
sar
eac
comp
lis
hedus
inggl
ycop
rot
eins
-CAM-c
ell
adhes
ionmol
ecul
e

-I
ntegr
algl
ycop
rot
einst
hats
pant
hec
ellmemb
rane

-Canb
indt
osi
mil
arCAM'
sfr
omnei
ghb
ori
ngc
ell
s(homot
ypi
cbi
ndi
ng)

-Canb
indt
odi
ffer
entCAM'
s(het
erot
ypi
cbi
ndi
ng)

-CAM'
sar
eimp
ort
antf
or:

1)Pr
operant
ibod
yfunc
tioni
nthei
mmunes
yst
em

2)Cel
l-c
ellc
onnec
tioni
nthener
vouss
yst
em

-Duri
ngemb r
yoni
cd ev
elop
ment
,cel
lad
hes
ioni
squi
ckl
yfol
lowedb
ythef
ormat
ionof
int
ercel
lul
arjunc
tions.

I
.Cel
ljunc
tions
-Sp
eci
ali
zedr
egi
onsofc
onnec
tionb
etweent
woc
ell
sorb
etweenac
ell
int
heext
rac
ell
ularmat
rix

1.Adhesi
vej
uncti
ons
-cel
l-c
ellj
unc
tiont
hathol
dsc
ellt
oget
heri
nhel
pmai
ntai
ncel
lsi
nthei
rfi
xed
posi
tioni
nti
ssues

a)2t
ypesofad
hes
ionj
unc
tions
:

1)Desmosome-s p
ecial
izedcell-c
elljuncti
onschar
acteri
zedbyd
ens
e
pl
aquesofp r
ot ei
nintowhi c
hi nt
er medi
atefil
amentsinthet
wo
adjoi
ningcel
linsertund erthecellmembrane

-Ab
und
anti
nski
n,mus
cle,andep
ithel
ial
cel
ls

a)Hemidesmosome(hal
fdesmosome)-i
sas pec
ial
izedc
ell
juncti
onbet weenacel
landthebasall
amina
(ext
racell
ularmatri
x)ofnei
ghbori
ngc el
ls
.

-Examp
le:c
oll
agenund
erl
yingep
ithel
ial
cel
ls

2)Ad
her
enj
unc
tions
-hear
tmus
cle,l
ineb
odyc
avi
ties

-Cel
ljunc
tioninwhi
chthecyt
opl
asmicf
aceofthe
pl
asmamemb ranei
satt
achedtoact
infi
lament
s

2.Tightjunc
tion-cel
l-c
ellj
unc
tionsthats
eal
sad
jac
entc
ell
stoget
her
,pr
event
ingt
hep
ass
ageofmos
t
di
ssolvedmol
eculesfromonesi
det ot
heother

3.Gap(communi
cati
ngjunct
ion)-cel
l-c
ellj
unc
tionthatal
l
owsi
onsands
mal
lmol
ecul
est
opas
sthe
cytop
las
mofonec el
ltothecytopl
asmofaneighbor
ingcel
l

Ext
rac
ell
ularmat
rix:

-Comp
lexnet
wor
kofp
oly
sac
char
idesandp
rot
einss
upp
ort
edb
ythec
ell

-Func
tions
:

1)Sup
por
t

2)Regul
ati
onofc
elld
ivi
sion

3)Ad
hes
ion

4)Cel
lmot
il
it
y

5)Cel
ldi
ffer
ent
iat
ion

-Comp
osedoff
iber
sands
urr
ound
ingnet
wor
k

-Fi
ber
s-l
ong,s
emic
rys
tal
li
neel
ement
satp
rov
ider
esi
stanc
etos
tret
chi
ng
-Net
wor
k-i
nter
loc
kedas
semb
lyofb
ranc
hedmol
ecul
est
hathol
dst
her
igi
dfi
ber
sinp
lac
e(el
ast
ic)

Ani
malext
rac
ell
ularmat
rix:

-Comp
osedofc
oll
agens(
fib
ers
);p
rot
eogl
ycans(
net
wor
k)=b
othgl
ycop
rot
eins

-Col
lagen-fi
ber
sprot
einri
chingly
cineandp
rol
inet
hati
samaj
orc
omp
onentoft
he
extr
ac el
lul
armatr
ixi
nconnec
t i
vetiss
ues

-Exi
stsi
nmanyf
orms
:

-Ty
peI
-(mos
tcommon)i
sfoundi
nski
n,t
end
on,andb
one

-Ty
peI
I-f
oundi
ncar
til
age

-Ty
peI
V-p
res
enti
ntheb
asall
ami
na

-Col
lagenc
omp
osedoft
hreeal
pha-hel
ic
alp
oly
pep
tid
echai
ns

-Al
phac
hai
nsr
egul
arl
ysp
acedgl
yci
ner
esi
dues

I
.As
semb
lyofc
oll
agen

-Sy
nthes
izeds
ecr
etor
ypr
otei
n

1.Al
phapoly
pepti
dechai
nsofc
oll
agenmol
ecul
ear
eas
semb
ledont
her
ibos
omesat
tac
hedt
omemb
ranes
oftheendopl
asmi
creti
cul
um

2.Car
bohy
drat
e,ol
igos
acc
har
ide,gr
oup
sar
ead
dedatt
heend
opl
asmi
cret
icul
umv
ias
pec
ifi
cenzy
mes

3.Col
lagens
ynt
hes
izedasap
rec
urs
ormol
ecul
ecal
ledp
roc
oll
agen

4.Pr
ocol
lagent
rans
por
tedt
otheGol
gic
omp
lexwher
eiti
spac
kagedi
ntos
ecr
eti
onv
esi
cl
es

5.Fus
ionoft
hev
esi
cl
eswi
tht
hep
las
mamemb
raner
eleas
est
hep
roc
oll
agent
othec
ell
ext
eri
or

6.I
nextrac
ell
ularr
egi
ons
,pr
oces
singenzy
mesr
emov
etheext
raami
noac
ids
equenc
esofp
roc
oll
agen
mol
ecul
es

-Pr
ocol
lagen(
sol
ubl
e)->c
oll
agen(
ins
olub
le)

I
I.Pr
oteogl
ycans

-Gl
ycop
rot
einswi
thhi
gh(
80%-90%)c
ont
entofc
arb
ohy
drat
es

-Macr
omol
eculesconsi
sti
ngofoneormoregly
c os
aminogl
ycanc
hai
ns(
GAG)at
tac
hedt
oa
cor
eprot
ein,whic
hi smodi
fiedb
ysul
fhy
dralgroups

-GAG-i
sanunb
ranc
hedc
hai
n,whi
chc
ons
ist
sofhund
red
sofr
epeat
ing2-s
ugaruni
ts

-Func
tionofp
rot
eogl
ycans
:
-Tr
apandi
mped
ethef
lowofwat
ermol
ecul
es

-Mos
tab
und
anti
ncar
til
age-p
rov
idesf
lexi
bil
it
yandel
ast
ici
tyt
othi
sst
ruc
tur
e

I
II.Mol
ecul
esl
inki
ngc
oll
agenandp
rot
eogl
ycanst
othec
ells
urf
ace

-Fi
bronec
tinandl
ami
ninar
egl
ycop
rot
eins

-Coll
agen,prot
eoglycans,fi
bronec
t i
n,andlami
ninc
anb
indt
oal
lsur
fac
erec
ept
orsc
all
ed
int
egrins-membrane-spanni
ngglycoprot
eins

-I
nt egrin-i
samemberofalar
gef ami
lyoftrans
memb
ranep
rot
einsi
nvol
vedi
nthe
adhesionofcel
lst
otheextr
acell
ularmatri
x

-Structurest
hatti
ecell
stotheext
rac
ell
ularmat
rixandal
sof
ormc
onnec
tionswi
tht
he
cyt
os kel
etonint
hecytopl
asm

-Manyi
ntegri
nsar
eus edi
nsignalt
rans
duc
tionp
athway
stot
riggeri
nter
nal
cel
lul
ar
res
pons
esf r
omexter
nalsti
muli

-I
ntegr
insp
layr
olesi
ncel
lgr
owt
h,c
elld
ivi
sion,andc
elld
iff
erent
iat
ion

-Oxidati
vep hosphorylati
on-pr
ocessi
nt hemit
ochondr
iai
nwhichATPformationi
sdr
iven
byt hetransferofel ectr
onsfromorganicmol
ecul
estomolec
ularoxy
gen.Proces
s
involv
est heintermed i
ategenerat
ionofap Hgradi
entac
rossamembraneand
chemiosmoticcoup l
ing

Res
pir
ati
on(
breat
hing)

I
.Comp
osedof
:

1.Gl
ycol
ysi
s(c
ytop
las
m)

2.Pent
osec
ycl
e(c
ytop
las
m)

3.Ci
tri
cac
idc
ycl
e(mat
rixofmi
toc
hond
ria)

I
I.Di
vid
edi
ntot
hreep
art
s:

1.As
eri
esofr
eac
tions
,whi
chp
rov
ideas
our
ceofel
ect
ronsat
,el
evat
edener
gyl
evel
s

2.Anel
ect
rontrans
portsys
tem,embeddedi
namemb
rane,t
hatus
est
heener
gyoft
heel
ect
ronst
obui
ld
aprot
ongrad
ientacros
sthemembrane
3.AnATP-s
ynthes
izedenzy
meemb
edd
edi
namemb
ranet
hatus
esap
rot
ongr
adi
entasanener
gys
our
ce
toconv
ertADPtoATP

I
II.Mi
toc
hond
rias
truc
tur
e:

-Memb
rane-b
oundc
ellor
ganel
let
hatc
arr
iesoutoxi
dat
ivep
hos
phor
ylat
ionandp
rod
ucesATP

1.Cont
ainst
wos
epar
atememb
ranes
yst
ems
,out
erandi
nnerb
ound
arymemb
ranes(
cri
stae)

2.I
nnermos
tcomp
art
menti
sthemat
rix

I
V.Oxi
dat
iver
eac
tions
:

1.Gl
ycol
ysi
s(Emb
den-Mey
erhof
fpat
hway
)

-Ubiqui
tousmetabol
icp
athwayi
nthecyt
osol(
cytopl
asmic)inwhi
chs
ugar
sar
e
inc
omp l
etel
ydegradedwit
hprod
ucti
onofATP"sugarspl
it
t i
ng"

1)I
n10s
tep
s,gl
ucos
eiss
pli
tinhal
fandc
onv
ert
edt
o23-c
arb
onac
ids(
pyr
uvi
cac
ids
)

A)2c
oenzy
mesar
ered
uced

B)Netf
ormat
ionof2ATPmol
ecul
es

C)Ori
ginalc
arb
ons1and6,2and5,and3and4ofgl
ucos
ebec
ome
equi
val
ent

2)Allenzy
mesar
esol
ubl
eandt
hewhol
epat
hwayi
scar
riedouti
nthe
cyt
op l
asm

3)Py
ruv
icac
idhi
ghl
yreac
tiv
eandp
roc
eed
stof
ormf
urt
herp
rod
uct
s

A)Sub
str
atef
ort
hec
itr
icac
idc
ycl
e(aer
obi
cres
pir
ati
on)

-Red
ucedc
oenzy
mei
sev
ent
ual
lyoxi
dizedb
yoxy
gen

B)Anaer
obi
cres
pir
ati
on:

-2t
ypes
:

1)Lac
ticac
idf
ormat
ion-

-Py
ruv
atei
sred
ucedt
olac
ticac
id

-Py
ruv
ate+NADH->l
act
ate+NAD+

-Occursinmus cl
ecel
ls
orheartc el
lsinani
mals
-temporarys t
oragefor
el
ectrons
 2)Al
cohol
fer
ment
ati
on(
yeas
t):

-Py ruvi
cac i
dis
decar b
oxylated
(releasescarbons3and
4)andr ed
ucedt oet
hyl
alcohol

-Py
ruv
ate+NADH->et
hyl
alc
ohol
+CO2
+NAD+

-Stri
ctanaerob
es-(
bac
ter
ia,f
ungi
)canp
rod
uceATPonl
yby
fer
mentation

-Facul
tati
veanaer
obes
-cans
wit
chb
etweenf
erment
ati
onandoxi
dat
ion
pathways

-St
ric
taer
obes
-unab
let
ocar
ryoutf
erment
ati
on

4)Thenetgai
nof2ATPmol
ecul
esp
ergl
ucos
eyi
eld
sfr
eeener
gy

-Pot
ent
ial
freeener
gys
til
linp
yruv
icac
id

-Yi
eld
sap
proxi
mat
ely2%

2.Ci
tri
cac
idc
ycl
e(p
yruv
ateoxi
dat
ion;TCAc
ycl
e;Kr
eb'
scy
cle)
:

-Cent
ral
met
abol
icp
athwayf
oundi
nal
laer
obi
cor
gani
sms

-Oxi
dizesac
ety
lgr
oup
sder
ivedf
roms
ugar
s(gl
ucos
e)t
oCO2andwat
er

-Oc
cur
sinmi
toc
hond
ria(
mat
rix)i
neukar
yot
icc
ell
s

1)Reacti
onsal
loc
c uri
nmitochondr
ia(orthememb
ranes
)st
art
ingwi
th
thesub
strate(
pyruvat
e)generatedincyt
oplas
m

2)Pathwayisacycl
eofr eac
tionsinvol
vingthei
nterc
onv
ersi
onof10
organi
cacid
s.CO2andr educ
ingp owerareformedfr
ompyruvi
caci
d,
withoneforcarb
onintermediatebeingusedupandoner
egenerat
edfor
eachturnofthecycl
e

-Remov est oelectr

ons,2hy d
rogens,andmovesone
carbon( CO2);acetylgr
oupst rans
ferredtocoenzymeA
acetylgr oups-energysour
cef orTCAcycl
e-elect
rons
fromNADH

1)Carb
onsrel
eas
edasCO2i
nthec
ycl
eder
ivesf
rom
carb
ons3and4ofgl
ucos
e

2)Pyruvateoxidati
onc at
alyzedbya
compl
exp rotei
nc al
ledpyruv
at e
dehy
dr ogenasecomp l
ex
 3)The2-c arbonp r
oductof
decar b
oxy l
ationofp y
ruvicac
id
condens eswitha4-c arbonaci
d
(oxaloaceticacid)toforma6-car
bon
acid,citri
cac id

4)Subsequently
,t hecarbonofpyruv
ic
aci
d(origi
nall
yc arbons2or5ofglucose)
andthenlastlythemet hy
l c
arbonof
pyruv
at e(fr
omc ar b
ons1or6ofgl ucos
e)
aremet ab
oli
zedt oCO2

-Thes
umoft
her
eac
tionsf
oronet
urnoft
hec
ycl
eis
:

+
1)Py
ruvate+3H2O+5c oenzymes +ADP
+Pi 3CO2+5coenzy
mes .H2+ATP

2)CO2isrel
easedasagasorsol
uti
on,
reduc
ingpowertransf
err
edtoelec
tron
trans
portchai
nt ooxy
gen

-El
ectronstr
ansf
eri
scoup
ledt
o
gener
at i
onofATP

3.Pent
ophos
phat
epat
hway(
pent
osep
hos
phat
eshunt
):

-Pat
hwaywher
egl
ucos
eisoxi
dizedandc
onv
ert
edt
oa5-c
arb
ons
ugar(
pent
ose)(
rib
ose-5-p
hos
phat
e)

-Pat
hwayal
sor
educ
esNADP+->NADPH

-Pat
hwaygener
atesr
educ
ingp
oweri
nthef
ormofNADPH

V.Mi
toc
hond
riael
ect
ront
rans
por
tsy
stem:

1.Cont
ains4lar
gep
rot
ein-b
asedc
omp
lexest
hatwor
kins
equenc
etod
eli
verel
ect
ronsf
romNADHand
FADH2tooxy
gen

2.Eac
hcomp
lexc
ont
ains
:

A)Amaj
orenzy
met
hatc
atal
yzesel
ect
ront
rans
fer

B)Nonprot
einorgani
cgroups(pr
ost
het
icgr
oup
s)t
hatd
irec
tlyexc
eptandr
eleas
e
el
ectronscar
riedbythecompl
ex

C)St
ruc
tur
alp
rot
einst
hatc
ont
rib
utet
omov
ementofp
rot
onsac
ros
sthememb
rane

-NADP+=ni
cot
inami
dead
eni
ned
inuc
leot
idep
hos
phat
e

-Coenzy
mec
los
elyr
elat
edt
oNAD+t
hati
sus
edext
ens
ivel
yinb
ios
ynt
het
icp
athway
s

-Ub
iqui
none-el
ect
ronc
arr
ier
3.Sys
temal
socontai
nst
woc
arr
ier
s,whi
chs
hut
tleel
ect
ronsb
etweent
hec
omp
lexes
:cy
toc
hromeC,and
ubi
qui
none(
coenzy
meQ)

A)4c
omp
lexes
:

-Comp
lexI
-cond
uct
sel
ect
ronsf
romNADHt
oub
iqui
none

-Comp
lexIc
ont
ains
:

A)Enzy
meNADHd
ehy
drogenas
e-oxi
dizesNADH

B)El
ectr
onsf
romNADHt
rans
fer
redt
oFMN(
pros
thet
icgr
oupb
oundt
o
comp
lex)

C)FMNH2oxi
dizedt
oub
iqui
none

-Compl
exIc
ont
ains>30p
rot
eins
;7enc
odedb
ymi
toc
hond
rial
DNA,r
estenc
odedb
y
nucl
eus

-FMN]
-fl
avi
nmononuc
leot
ide

-FAD-f
lav
inad
eni
ned
inuc
leot
ide

-(
Vit
ami
nB)r
ibof
lav
in->2p
hos
phat
es->r
ibos
e->ad
eni
ne

-Red
ucedf
ormb
yad
dinghy
drogenst
ocent
ral
nit
rogenofi
soal
loxazi
ne
ri
ng

-Comp
lexI
I-c
arr
iesel
ect
ronsf
roms
ucc
inat
e(TCAc
ycl
e)t
oub
iqui
none

-Comp
lexI
Icont
ains
:

A)Enzy
mes
ucc
inat
edehy
drogenas
e(c
atal
yzesr
eac
tion6ofTCAc
ycl
e)

-Suc
cinat
e->f
umer
ate

B)El
ect
ronst
rans
fer
redt
oFAD->ub
iqui
none

C)Contai
nsthreepol
ypep
t i
desubuni
ts+(cont
aini
ron
andsul
fur)(i
ron/s
ulfurcenter
s)+succi
nate
dehy
drogenase

D)Al
l4s
ubuni
tsenc
odedi
nthec
ell
nuc
leus

-Comp
lexI
II-c
ond
uct
sel
ect
ronsf
romub
iqui
nonet
ocy
toc
hromeC

-Comp
lexI
IIc
ont
ains
:

A)Cyt
ochr
omeCr eductas
e-cat
alyzestr
ans
ferof
el
ect
ronsfromub
iquinonetocytoc
hromeC
 B)Contai
ns11p ol
ypepti
des
:1(c
ytochr
omeB)enc
odedb
y
mit
ochondri
alDNA,otherir
on/sul
fursub
uni
ts

-Comp
lexI
V-c
ond
uct
sel
ect
ronsf
romc
ytoc
hromeCt
ooxy
gen

-Comp
lexI
Vcont
ains
:

-4s
ubuni
ts+13p
oly
pep
tid
es

A)Cy
toc
hromeA

B)Cy
toc
hromeA3

C)2coppercentersubuni
tsCuAandCuBl
inkedby3
pol
ypep
tides(I,II,I
II)IIIenc
odedbymi
tochond
rial
DNA

-10ad
dit
ional(
auxi
li
arys
ubuni
ts)enc
odedb
ynuc
learDNA

VI
.Pr
otonp
ump
ingb
yel
ect
ront
rans
por
tchai
n:

1.Mi
toc
hondri
alel
ect
ronst
rans
portsys
tempumpspr
otonsfromt
hemat
rixi
ntot
hei
nter
memb
rane
comp
artmentasel
ectr
onsfl
owfromNADH/FADHtooxygen

A. 4protonsarepushedacros
st heinnerbound
arymemb
raneas2el
ect
ronsmov
ethr
ough
compl
exI
B. Frommat r
ixtointermembranecomp ar
tment

2.Twop
rot
onsus
etwoel
ect
ronsmov
ethr
oughc
omp
lexesI
IorI
V

3.Protongradi
entdev
elopedt
hr oughelec
tront
rans
por
tist
heener
gys
our
cef
ort
heF0F1-ATPas
e(ADP+
phos
p hate ATP)
-catal
yzesthec onv
ersi
on

St
ruc
tur
eofF0F1ATPas
e(ad
enos
inet
rip
hos
phat
ase)
:

-Canb
esep
arat
edi
nto2s
ubp
art
sF0andF1

-F1-c
oup
lingf
act
or1

-F0-ol
igomy
cin-s
ens
iti
vef
act
or-d
rugt
hati
nhi
bit
sATPas
e

-F0F1ATPas
eisal
oll
ipop
-shap
edp
art
icl
e

-Cont
ainsahead
piec
econnec
tedt
oab
asaluni
tors
tal
k

-F1-s
iteofATPs
ynt
hes
is

-F0-s
upp
liesp
rot
ons(
memb
ranec
hannel
)

-F0F1ATPas
eofE.
col
icont
ains8s
ubuni
ts
-F1hasf
ives
ubuni
ts

-F0hast
hrees
ubuni
t-p
rot
onc
hannel
scomp
osedof6-12Cs
ubuni
ts

Phot
osy
nthes
is:

-Proces
sinwhichl
ightenergyi
sab
sor
bedb
ysp
eci
ali
zedp
igment
sofac
ell
andi
s
convert
edtochemi
c alener
gy

1.Comp
osedofl
ightandd
arkr
eac
tions

-Li
ghtr
eac
tions
-requi
resl
ight

-Phot
ored
uct
ion-p
rod
uct
sar
ered
ucedc
arr
ier
sandoxy
gen

-Nonc
ycl
icp
hot
ophos
phor
ylat
ion-ATP

-Cy
cli
cphot
ophos
phor
ylat
ion-GTP

-ATPandr
educ
edc
arr
ier
sar
eus
edi
ndar
kreac
tionst
oconv
ertCO2t
ocar
bohy
drat
es

-Conv
ers
ionofi
nor
gani
cCO2t
oor
gani
ccomp
ound
s

2.Pr
oces
sineukar
yot
es(
plant
sandal
gae)oc
cur
sinc
hlor
opl
ast
s

-Memb
rane-b
oundor
ganel
leswher
etheb
ioc
hemi
calc
onv
ers
ionofl
ightener
gyt
oATPoc
cur
s

I
.St
ruc
tur
eofc
hlor
opl
ast
s:

1.Sur
round
edb
ytwoc
ont
inuousmemb
ranes
,out
erandi
nnerb
ound
arymemb
ranes

-Memb
ranes
epar
atedb
yint
ermemb
ranec
omp
art
ment

2.Bound
arymemb
ranesenc
los
eani
nnerc
omp
art
mentc
all
edt
hes
troma(
anal
ogoust
omi
toc
hond
ria
matri
x)

3.Wi
thi
nst
roma,t
her
eisat
hir
dmemb
ranes
yst
emc
ons
ist
soff
lat
teneds
acksc
all
edt
hyl
akoi
ds

4.Thy
lakoi
dsr
angedi
nst
acksc
all
edgr
ana

5.St
acksar
econnec
tedb
ymemb
ranec
all
eds
tromal
lamel
lae

I
I.Thel
ightr
eac
tions
:

1.Li
ghtenergy(photons
)isabsorb
edbyp
igmentmol
ecul
esi
nthechlor
oplasts(c
hlor
ophyl
l
)caus
ing
el
ectronsi
nt hei
rgroundstat
et omov
etoanewor b
ital
ofhi
gherenergy(exci
tedstat
e)

A)Inphot
osynthes
is,l
ighti
sconv
ertedtochemi
cal
energythroughthetr
ansferof
el
ectr
ons,exci
tedbywhiteabs
orpti
oninchl
orop
hyl
l,t
os t
ableorbi
tinpr
imar
yr ecep
tor
mol
ecul
es

B)Als
oexistaccess
orypigmentmol
ecul
esi
nad
dit
iont
ochl
orop
hyl
l,whi
chc
anab
sor
b
l
ightener
gyc al
ledcar
otenoids

1)Pas
sener
gyt
ochl
orop
hyl
lmol
ecul
es

-Chl
orophy
llandcar
otenoi
dsarel
ipid
sboundt
o
thyl
akoi
dsmemb r
anesandstr
omallamel
lae

-Chl
orop
hyl
lsar
emol
ecul
esb
asedonat
etr
apy
rol
eri
ng

-2maj
orc
hlor
ophy
ll
saandb

-El
ect
ronsi
nri
ngc
anab
sor
bli
ghtatd
iff
erentwav
elengt
hs

2)Li
ghtr
eac
tionsor
gani
zedi
nto2c
omp
lexes
:phot
osy
stemIandp
hot
osy
stemI
I

-Eac
hsy
stem(
inc
hlor
opl
ast
s)c
ont
ain:

A)50to100chl
orop
hyl
lamol
ecul
esp
lusas
mal
lnumb
er
ofcar
otenes

B)20poly
p ep
tid
esc ar
ryouts
truc
tur
al,enzy
mat
ic,and
regul
atoryfuncti
ons

-Reactioncenter-one
or2c hlorop
hy l
la
moleculeswithinthe
photosystemswher e
excit
edel ect
ronsare
transferredtos t
able
orbi
tals

C)Alsoc ontai
nasequenceofc
arrier
moleculesthatareinv
olv
edinthe
transportofelect
ronsawayfrom
primaryac c
eptor
s

D)Photosyst
emI Icontai
nst he
mechanismforspl
it
t i
ngwat erinto
protons
,electr
onsandoxy gen,thi
sis
call
edphotol
ysi
s

E)Light -harvesti
ngcompl
exes(LHCs)-
int
er nal memb r
anesofchl
oropl
asts,
whichc ontainp i
gment-pr
otein
assemb l
iest hatactasacc
essoryli
ght-
gathering" antennas"

-Donothaver
eac
tionc
ent
ers/p
rimar
y
accep
tors
 -Donotc
onv
ertl
ightt
ochemi
cal
ener
gy

-Passonenergyofab
sor
bli
ghtt
othe
tophotos
ystems

-LHC-1-as
soc
iat
edwi
thp
hot
osy
stemI

-LHC-2-as
soc
iat
edwi
thp
hot
osy
stemI
I

2.St
ruc
tur
eofp
hot
osy
stemI
:

A)Contains110chl
orophyl
lamolecul
es+16b
et a-c
arot
enes+21ad
dit
ionalp
rot
einsi
na
l
ight-abs
orbings
t r
ucturecal
ledthecor
eantenna

B)Li
ghtenergypassedfromcor
eantennatothereac
tioncent
er-s
pec
ial
izedc
hlor
ophy
ll
amolec
ulecal
ledP700-ab
s or
bsl
ightmaxi
mal
lyatwavelengt
h=700nm

3.St
ruc
tur
eofp
hot
osy
stemI
I:

A)Cont
ains40c
hlor
ophy
llamol
ecul
es+b
eta-c
arot
enes+22p
rot
eins

B)Reac
tionc
ent
erc ont
ainsasp
eci
ali
zedf
ormofc
hlor
ophy
lla,P680-ab
sor
bsl
ight
maxi
mall
yatwavel
engthof680nm

C)Phot
oly
sisas
soc
iatedwit
h3p
eri
pher
alp
oly
pep
tid
esand4manganes
eat
omsc
omp
lexed
i
ntoamanganesecenter

-Cal
ci
umandc
hlor
inenec
ess
aryc
ofac
tor
sfort
hec
ent
er

4.St
ruc
tur
eoft
hel
ight
-har
ves
tingc
omp
lexes(
LHCs
):

A)LHC-1compl
ex(antenna)cont
ainsab
out80t
o120mol
ecul
esofc
hlor
ophy
llaand
chl
orophy
llb+fourpol
ypepti
des

B)LHC-2compl
excont
ainsabout50c
hlor
ophy
llaandbmol
ecul
es(
1:1r
ati
o)+4
pol
ypept
idesp
lusabeta-car
otene

-Ener
gyofp
hot
onsab
sor
bedb
ytheLHCsi
spas
sedt
hrought
he2p
hot
osy
stems

C)El
ect
ront
rans
por
tsy
steml
inkst
he2p
hot
osy
stems

-2photosys
temsareli
nkedi
nchlorop
lastsb
yanel
ect
rontransp
ort
sys
temt hatcond
uctsel
ectr
onsfromones ys
temt
othenextanddel
iver
s
el
ectronstoNADP+attheendofthep at
hway

-Phot
osy
stemsar
ear
rangedi
naZ-p
athway

5.Zp
athway
:

A)El
ect
ronsenterp at
hway(photos
yst
emI
I)f
romt
heb
reakd
ownofwat
ert
opr
otons
,
el
ect
rons,andoxygen(phot
olys
is)
 1)Car
riedtor
eac
tionc
ent
erb
yel
ect
ronc
arr
ierZ-wat
er->el
ect
rons->Z->P680->
P680(
excit
ed)

-Z+t
yros
iner
esi
dueonD1p
oly
pep
tid
e

2)Afterexc
itati
on,electr
onst ravelf
romP680toaprimar
yrecep
torof
photosy
stemII(Qa)(p l
astoqui
none)->2ndplas
toqui
none(Qb
)(fi
nal
elec
troncarri
erinphotosystemI I
)

B)El
ect
ronsmov
efr
omQbt
oap
oolofp
las
toqui
nonemol
ecul
es(
PQp
ool
)

-Anal
ogoust
oqui
nonec
arr
ieri
nmi
toc
hond
ria

-El
ect
ronsmov
efr
omPQp
oolt
o3c
arr
ier
s

-Cy
toc
hromeb
6

-I
ron/s
ulf
urp
rot
ein

-Cy
toc
hromef
-rel
atedt
ocy
toc
hromeC

-B6/fc
omp
lex-anal
ogoust
ocomp
lexI
IIofmi
toc
hond
rial
sys
tem

-Elec t
ronsmovefromb 6/fcompl
extofinalcar
rierwhichl
inksthe
phot osys
tems,pl
astoc
y ani
n(PC)
-shutt
leselect
ronsfromb6/fc ompl
ex
top hotosys
temI-analogoustoc
ytoc
hromeCofmi t
ochondr
ialel
ec t
ron
trans por
tsystem

C)El
ect
ronsf
lowf
romPCt
oP700c
hlor
ophy
llatr
eac
tionc
ent
erofp
hot
osy
stem1

1)Aft
erexci
tati
onbyli
ght
,elect
ronsaretransf
erredf
romP700t o
pri
maryrec
eptorofp
hotosy
stems.I(modi
fiedc
hlor
ophyl
lcal
ledA0)

2)El
ect
ronsf
lowf
romA0t
oA1,aqui
noned
eri
vedf
romv
itami
nK

3)El
ect
ronst
henf
lowt
hrough3i
ron/s
ulf
urc
ent
ersi
nphot
osy
stem1

4)El
ectr
onsp as
sf romphotos
yst
em1t oproduc
tion,ani
ron/s
ulf
ur
prot
einthatacces
sas epar
ateelec
tronc
ar e

5)El
ect
ronp
air
sfr
omf
err
edoxi
ntoFADt
oNADP

-FADi
sac
oenzy
me,whi
chi
spar
toff
err
edoxi
n-NADPoxi
dor
educ
tas
e

I
II.Feat
uresofp
hot
osy
nthes
is:

1.El
ect
ronsr
ecei
ve2i
nput
sofener
gy

-Ener
gyr
educ
esNADP

-Us
edt
oes
tab
li
shp
rot
ongr
adi
ent(
prot
onp
ump
sfr
omt
hes
tromai
ntot
het
hyl
akoi
dsc
omp
art
ment
s)
-Onei
nphot
osy
stemI
I

-Onei
nphot
osy
stemI

2.El
ectronflowintheZp
athwayf
romwat
ert
oNADPi
scal
lednonc
ycl
icp
hot
osy
nthes
is(
nonc
ycl
ic
phot
ophosphoryl
ati
on)

3.Pr
oces
sofp
hot
oly
sisut
il
izeswat
erasanel
ect
rons
our
ce

-Al
sop
rod
ucesoxy
gen

4.El
ect
ronsc
anal
sof
lowi
nac
ycl
ewi
thi
nac
los
edc
irc
uitofp
hot
osy
stem1(
cyc
li
cphot
ophos
phor
ylat
ion)

-El
ect
ronsf
lowf
romf
err
edoxi
nbac
ktot
heb
6/fc
omp
lex(
ins
teadofgoi
ngt
oNADP+)

-Cy
clep
ump
sad
dit
ionalp
rot
onseac
hti
meel
ect
ronsf
lowt
hrought
heb
6/fc
omp
lex

-Pr
otongrad
ientdriv
esthesynt
hes
isofoneATPmol
ecul
eforeac
hel
ect
ronp
air
,thus
,
ATPisf
ormedwithoutred
uct
ionofNADP+

5.Pr
otongr
adi
entofZp
athway
:

-Pr
otonp
rod
ucedd
uri
ng:

A)Phot
oly
sis

B)Aselec
tronsp
assf
romf
err
edoxi
ntoNADPv
iaf
err
edoxi
n-NADPoxi
dor
educ
tas
e
car
rier

C)Asel
ect
ronsf
lowt
hroughb
6/fc
omp
lex

6.Chl
orop
las
tsus
ethep
rot
ongr
adi
entt
opr
oduc
eATP

-Cont
ainsaCF0-CF1ATPas
e(s
imi
lart
oF0F1ATPas
einmi
toc
hond
ria)

7.Summar
yofp
hot
osy
nthes
isandt
hec
hemi
osmot
ichy
pot
hes
is

-Pr
opos
edb
yDr
.Mi
tchel
lin1962-c
onnec
tionb
etweenp
rot
ongr
adi
entandATPs
ynt
hes
isi
nchl
orop
las
ts

A)Sup
por
tingf
eat
ures/ev
idenc
e:

1)Photophos
phor
ylat
iond
epend
sont
hep
res
enc
eofc
los
edmemb
ranousv
esi
cl
es
(chl
oropl
asts)

2)Electrontransp
or tthroughp hotos
yst
emI Iandphotosyst
em1,or
cycl
ictransportaroundp hotosystem1,res
ultsi
nanac cumulati
onof
protonsinsi
deisol
atedt hylakoi
dsorenzymevesic
lesderiv
edf r
om
thyl
akoids

3)Destr
uctionoft
hep r
otongr
adientbyagentsthatinc
rease
permeabi
li
tyofthyl
akoi
dmembranestoprotonss
t op
sATPs y
nthes
is
-I
mpos
iti
onofanar
tif
ici
alp
rot
ongr
adi
entac
ros
sthy
lakoi
dmemb
raness
timul
atesATPs
ynt
hes
is

I
V.Dar
kreac
tions
:

-Chemic
alener
gyproducedi
nt hel
ightreacti
onsi
susedinthedarkreacti
ons(
donot
requi
reli
ght)t
oconvertCO2intocarbohyd
rateandotheror
ganicpr
od uc
ts

-Requi
rep
rod
uct
sofl
ightr
eac
tions(
ATP/NADPH)

-Cal
vincy
c l
e(Calv
in-Bensoncy
cle)
-majormetabol
icp at
hwaybywhi
chCO2i
sfi
xedd
uri
ng
phot
osynthesi
s,C3cycle-us
esCO2,ATP,NADPHasr eactant
s

-Rel
eas
esADP,NADP+,and3PGALasp
rod
uct
s

-8s
tepp
athway

-Tr
ans
ket
olas
e-t
rans
fer
s2c
arb
onmol
ecul
esf
romones
ugart
oanot
her

-Tr
ans
ald
olas
e-t
rans
fer
s3c
arb
onmol
ecul
esf
romones
ugart
oanot
her

-Al
dol
ase-t
rans
fer
sdi
hyd
roxy
acet
onep
hos
phat
etoav
ari
etyofal
dehy
des

1.C4c
ycl
e:

-Al
ter
nat
ived
arkr
eac
tionp
athway

-Duet
othef
actt
hatt
hekeyr
egul
ator
yenzy
meRUBI
SCOc
anal
soac
tasanoxy
genas
e

-C4c
ycl
ecankeepCO2b
acki
ntot
heC3c
ycl
e

-C4c
ycl
eoc
cur
swhenoxy
genl
evel
sar
ehi
ghi
npl
ant
s

-Oxy
gens
timul
atesoxy
genasac
tiv
ityofRUBI
SCO

-Onep
rod
uctofs
upp
ortp
athway
,mal
ate,d
iff
usest
ocel
lwher
eoxy
genl
evel
sar
elow

-Mal
ate->p
yruv
atewi
thl
ossofCO2,whi
chent
ersC3c
ycl
einc
ell
swher
eoxy
genc
ont
enti
slow

Mi
crot
ubul
es:

I
.Twos
truc
tur
esi
nvol
vedi
ncel
lmov
ement
:

1)Mi
crot
ubul
es-unbr
anchedcyl
ind
ersab
out25nmi
ndi
amet
erwi
thanop
enc
ent
ral
channel
andi
s
comp
osedoft
ubuli
n(prot
ein)
2)Mic
rofi
lament
s-areext
remel
yfi
neunb
ranc
heds
oli
dfi
ber
sab
out5-7nmi
ndi
amet
erandar
ecomp
osed
ofthepr
ot ei
nacti
n

-Bot
hac
tsep
arat
elyandt
oget
hert
opr
oduc
ecel
lul
armov
ement

-EX:

1)Fl
agel
la/
cil
iab
eat
ing-mi
crot
ubul
es

2)Mus
clec
ont
rac
tion-mi
crof
il
ament
s

3)Cy
top
las
mics
treami
ng-mi
crof
il
ament
s

4)Mov
ementofmi
toc
hond
ria/
ves
icl
es-mi
crot
ubul
es

5)Bot
hinv
olv
edi
ncel
ldi
vis
ion

-Mi
crot
ubul
esd
ivi
deandd
ist
rib
utec
hromos
omes

-Mi
crof
il
ament
sdi
vid
ethec
ytop
las
m

-Mol
ecul
armec
hani
smsf
ormov
ementoc
curt
hroughanac
tiv
esl
idi
ng

I
I.Mi
crot
ubul
est
ruc
tur
e:

-Cons
ist
sofac
irc
leof13s
pher
icals
ubuni
ts

-Sub
uni
tsl
ineupi
npar
all
el,l
engt
hwi
ser
owsc
all
edp
rot
ofi
lament
s

-Thes
epr
otof
il
ament
sfor
mawal
l

-Eac
hwal
lpar
tic
lei
sauni
toft
ubul
in

-Het
erod
imerof2t
ubul
inp
rot
eins(
alp
ha&b
eta)

-Mi
crot
ubul
esc
anoc
curasd
oub
let
sort
rip
let
s

-Consi
s tofonecomp
letemic
rot
ubule(
13subuni
ts)wit
hone(
doub
let
)ort
wo(
tri
plet
)
parti
al,C-shap
edmicrot
ubul
esfus
edtoitatonesid
e

-Doub
let
soc
curi
nfl
agel
la/
cil
ia

-Tri
plet
soccurincentr
iol
es(
str
uct
urest
hatgi
ver
iset
ofl
agel
laandanc
hort
hemi
nthe
cyt
oplasm)
/basalb
odies

1.As
semb
lyofTub
uli
nint
oMi
crot
ubul
es:

-Rev
ers
ibl
ereac
tiont
hati
sinequi
li
bri
um

A)Dep
end
sonc
onc
ent
rat
ionof
:
 1)GTP

+
2)Ca2

c
)pH

2.Mi
crot
ubul
e-as
soc
iat
edp
rot
eins(
MAP’
s):

A)Oneendofami
crot
ubul
ecanas
semb
leord
isas
semb
le2t
o4t
imesf
ast
ert
hant
heot
her=p
olar
ity

-Theendwi
tht
hef
ast
err
ateofas
semb
lyord
isas
semb
lyi
sthep
lusendofami
crot
ubul
e

-Theendwi
tht
hes
lowerr
atei
sthemi
nusend

B)St
ablemic
rot
ubulesc
anac hi
eveabal
ancepoi
ntatwhi
cht
ubul
inhet
erod
imer
sad
dto
thep
lusendwhi
letheminusendisd
isas
sembl
ing

-Heter
odimerscanmigrat
ethroughamic
rot
ubul
eort
read
mil
lthr
ougha
micr
otubulef
r omoneendtotheother

C)Largescalep
roduct
ionofmi
crot
ubul
esoc
curi
ndi
sti
ncts
truc
tur
esc
all
edmi
crot
ubul
e
organi
zingcent
ers(MTOC’
s)

-Ther
ear
e4t
ypes
:

a)Cent
riol
es(
bas
alb
odi
es)
-gener
atemi
crot
ubul
esoff
lagel
la

b)Cellcenter
s(cent
rosomes/
asters
)-d
ensemateri
al
l
ocatedneart henucl
eusandorgani
zecyt
opl
asmic
micr
ot ubul
es

c
)Ki
netoc
hores-plat
e-l
ikes
truc
tur
esont
hes
urf
aceofc
hromos
omes
(
nuc
leard
ivi
sion)

d
)Spind
lepol
ebodi
es-gi
veris
etostruc
ture(sp
ind
les
)in
f
ungalcel
lst
hatareinv
olv
edinnuc
leardi
vis
ion

-MTOC’
spr
ovi
deanuc
leat
ionc
ent
erf
orhet
erod
imerp
oly
mer
izat
ion

3.Funct
ionofMi
crot
ubul
es-c
onv
ertc
hemi
calener
gyt
omec
hani
cal
ener
gyb
ysl
idi
ng=i
nvol
vedi
ncel
l
movement

-Dy
nein-memberofafamil
yofl
argemotorprot
einsthatunder
goATP-d
epend
ent
movemental
ongmicrot
ubul
esvi
aac r
oss
b r
idgecycl
ingevent

-Comp
osedof2ar
msext
end
ing

4.Cr
oss
bri
dgemec
hani
sm(
hyp
othes
is)
:

A)Dynei
narmsundergoconf
ormati
onalchangest
hatadjus
tthei
rangl
eofat
tac
hment
tothemicr
otub
ulesurfac
ebetweenappr
oximatel
y90’and45’
B)ATPb
ind
ing,b
utnothy
drol
ysi
s,i
srequi
redt
orel
eas
edy
nei
nar
msat
tac
hedi
nthe90’
pos
iti
on

C)ATPi
shydr
oly
zedats omepoi
ntaf
t err
eleas
eofd ynei
nar
ms;hy
drol
ysi
spr
eced
esor
acc
ompani
esmovementofthearmstothe45’pos
iti
on

5)Releaseofthepr
oduct
sofATPhydr
olys
is(ADP+Pi)doesnotoc
curunt
ild
ynei
nar
ms
reat
tac htoanadj
acentmic
rot
ubul
eafterATPhydroly
sis

5.St
ruc
tur
eofMi
crot
ubul
esi
nFl
agel
la/
Cil
ia:

-Consi
stofacir
cleofninef
used,d
oubl
emicr
otubules
,theper
ipherald
oublets,ar
ranged
around2cent
ralmicr
otubul
es,t
hecent
rals
ingl
ets=9+2sys
tem(flagel
laraxoneme)

A)Eac
hoft
he2c
ent
ral
singl
etsi
sac
omp
let
emi
crot
ubul
e

B)Peri
pherald
oub
let
scont
ainonec
omp
let
eMT(
Asub
tub
ule)andonep
art
ialMT(
B
subt
ubule)

C)Connec
tingel
ement
s:

1)Cent
rals
ingl
etsc
onnec
tedb
yab
rid
geandas
urr
ound
ings
heat
h

2)Asubt
ubul
eofeac
hdoub
leti
sconnec
tedt
othec
ent
ral
sheat
hbya
spoke

3)Nexi
nlinkconnec
tsper
ipher
aldoub
let
s-Asubtub
ule
ofonedoubl
ett oBsub
tubul
eofthenextdoub
let

D)Dy
nei
nar
msc
onnec
tedt
oAs
ubt
ubul
edoub
let

E)Microtubul
esofc
il
iaandf
lagel
laar
isef
roms
truc
tur
esorb
asalb
odi
esc
all
ed
cent
rioles

1)Cent
riol
esc
ont
ainar
elat
ed9+2s
yst
em

2)Ni
nes
etsoft
rip
letMT’
smakeupt
heout
erc
irc
leoft
hec
ent
riol
e

-As
ubt
ubul
e=c
omp
let
eMT

-B&Cs
ubt
ubul
es=p
art
ialMT’
s

Mi
crof
il
ament
s:

-Ac
tinf
il
ament
s

I
.Func
tioni
n:

1)Cy
tos
kel
etals
upp
ort

2)Mov
ement
 a)Cy
t op
las
micstr
eaming-s
egment
soft
hec
ytop
las
mfl
owac
tiv
elyandd
irec
tional
lyf
rom
oneregi
onofanother

b
)Cont
rac
tion-s
li
dingmi
crof
il
ament
sfor
cib
lyc
ons
tri
ctors
hor
tenc
ell
segment
sorwhol
ecel
ls

I
I.St
ruc
tur
eofMi
crof
il
ament
s:

1)Ac
tin-ab
und
antp
rot
eint
hatf
ormsMF’
sineukar
yot
icc
ell
s.

-Themonomer
icf
ormi
scal
ledgl
obul
arorG-ac
tin;t
hep
oly
mer
icf
ormi
sfi
lament
ousorF-ac
tin

-Ac
tinc
anp
oly
mer
izet
oMF’
s

-Pol
ymer
shav
epol
ari
ty(
rat
esofas
semb
ly)
(si
mil
art
oMT’
s)

-Pl
usendad
dss
ubuni
ts12xf
ast
ert
hanmi
nusendd
isas
semb
less
ubuni
ts

-Pol
ari
tyc
anb
edet
ermi
nedb
ymy
osi
ndec
orat
iond
evel
opedb
yDr
.Huxl
eyi
n1963

-Myos
indecor
ation-MFreact
edwithmyosi
n,whi
chprod
ucesan
"ar
rowhead
"p at
t er
nthatischar
acter
ist
icofmi
crof
il
aments

-Ref
lec
tbi
ndi
ngofmy
osi
nsegmentt
oac
tin

-"
Arr
ows
"poi
ntt
owar
dthemi
nusendofaMFort
he"
poi
nted
"end

-Op
pos
iteend"
plus
"isc
all
edt
heb
arb
edend

2)Ac
tinb
ind
ingp
rot
eins(
ABP’
s)

-Ther
ear
e>60ABP’
swhi
chf
unc
tiont
oshi
ftp
oly
mer
izat
ionr
eac
tionst
ounas
semb
leds
ubuni
ts

-Bl
ocki
ngp
oly
mer
izat
ion

-Cap
pingMFs
ubuni
ts

-Sev
eri
ngorb
reaki
ngMFs
ubuni
ts

A)ABP’
sregul
atedb
y:

+
Ca2 /
1) cal
mod
uli
ncomp
lex

2)Phos
phor
ylat
ion(
kinas
es)

-Myosi
n-typ
eofmot orp
rot
einthatus
esATPt
odr
ivemov
emental
ongac
tinf
il
ament
s(7
cl
assesofmyos
in)us
ingacros
sbri
dgecyc
le

-Myosi
nI-iswi
del
ydi
str
ibut
edwi
thi
nthec
ell
,of
tenmemb
rane-b
ound
,andi
snotas
semb
ledi
nto
fi
laments

-My
osi
nII
-isav
eryl
argep
rot
eint
hatf
ormst
het
hic
kfi
lament
sofs
kel
etal
mus
clet
hat
 s
li
deov
erac
tinf
il
ament
sdur
ingc
ont
rac
tion

3.My
osi
n:

A)Compos
edof1or2lar
gep ol
ypept
idec
hai
ns"
myos
inheav
ychai
ns"and1or2s
mal
ler
pol
ypep
tid
echai
ns"my
osinl
ightchai
ns"

B)Heav
ychai
nsc
omp
osedofaheadandt
ail
;thel
ightc
hai
nsas
soc
iat
ewi
tht
hehead

C)Headc
ont
ains
:

-Ac
tinb
ind
ings
ite

-Hy
drol
yzesATP->ADP

D)My
osi
nIIc
anb
esp
liti
nto2p
art
sbyp
rot
ein-d
iges
tingenzy
mes(
prot
eas
e)s
uchast
ryp
sin

-Headf
ragment=heav
ymer
omy
osi
n(HMM)f
ragment-c
ont
ainsATPas
eac
tiv
ity

-Tailf
ragment=l
ightmeromyos
in(LMM)contai
nsbind
ingsi
testhat
assemblemyos
inI
Iintosuper
struc
turesc
alledthi
ckfil
aments

4.My
osi
nCr
oss
bri
dgeCy
cle:

-I
sanat
tac
h-p
ull
-rel
eas
ecy
cle,whi
chgener
atesMF-b
asedmot
ion

-Cy
clei
sthep
owers
our
cef
ormi
crof
il
aments
li
dingwhi
chi
sres
pons
ibl
eformus
clec
ont
rac
tion

-Si
mil
art
ocr
oss
bri
dgemec
hani
smut
il
izedb
yMT’
s

A)Regul
ati
onofc
ros
sbr
idgi
ng:

-2p
athway
sregul
atemy
osi
ncr
oss
bri
dgi
ngc
ycl
e:

1)Acti
n-l
inkedregulati
on-i
nvol
vespr
oteinst
hatbindt
oacti
nandf
orm
regul
ator
yunitslocatedonthesur
facesofmic
rof
il
aments

a)Acti
n-l
inkedr
egul
ati
on-d
epend
son2p
rot
eins
,tr
opomy
osi
nand
trop
onin

-Thesetwop rotei
nscontr
ol the
crossb
ridgi
ngc ycl
ebyundergoingCa++-
dependentconformati
onalchanges

-Changesal
ter
natel
ybloc
kandexp os
e
thesit
esonacti
nboundbymy os
in
duri
ngt hec
ross
bri
dgi
ngc y
cle

2)My
osi
n-l
inkedr
egul
ati
on-b
asedont
her
egul
ator
ymy
osi
nli
ghtc
hai
ns

a)Bot
har
econt
rol
ledb
y[Ca++]i
ncy
top
las
m
 Ca2+i
1) onsb
indt
ocal
mod
uli
n

2)Calmodulinundergoesa
conformationalc
hangeandac t
ivat
es
themy osi
nl i
ghtchainkinas
e(MLC
kinase)

3)Acti
vatedMLCkinaseaddsPO4group
s
deri
vedfromATPtot hemyosi
nlight
chai
ns-cr
ossbri
dgi
ngc yc
leistur
ned
"on"

4)IfCa2+isrel
easedf r
omc al
moduli
n,
thereisaninhib
itionofMLCkinase
acti
vit
y( nophosphoryl
ati
onactiv
ity)

5)PO4groupsareremov
edfromthe
regul
atoryl
ightchai
nsbyanenzyme
MLCphosphatase

6)Cr
oss
bri
dgi
ngs
top
s

Cy
tos
kel
eton:

-Comp
osedofMT’
s,MF’
s,I
F’sandad
dit
ionals
upp
ortp
rot
eins

-Ext
endf
romp
las
mamemb
ranet
othenuc
learenv
elop
e

-1/
3oft
otal#ofp
rot
einsar
ecy
tos
kel
etalp
rot
eins

I
.Int
ermed
iat
eFi
lament
s:

-Di
amet
erof10nm(
bet
weenMFandMT)

1.5c
las
sesi
nani
malc
ell
s:

A)Ker
ati
n-ep
ithel
ialc
ell
s,l
ineb
odyc
avi
ties

B)Vi
ment
in-b
lood
,bone,c
art
il
age

C)Des
min-mus
cle

D)Neur
ofi
lament
-neur
ons

E)Gl
ialf
il
ament

-Ob
ser
vedi
nver
teb
rat
es,i
nver
teb
rat
es,s
li
memol
ds,p
rot
ozoa,b
utnotp
lant
s

2.Fi
lament
sas
semb
ledf
romav
ari
etyofp
rot
eins
:

A)Cy
toker
ati
ns
B)Vi
ment
in

C)Des
min

D)Neur
ofi
lament

E)Gl
ialf
ibr
il
lar
yac
ids

3.As
semb
lyofI
nter
med
iat
efi
lament
s:

A)Sub
uni
tsas
semb
lei
ntoat
etr
amer(
cons
ist
sof2c
oil
ed-c
oil
edp
oly
pep
tid
echai
ns)

-Tetr
amerass
oc i
atetoformaprot
ofi
lament,whi
chi
sanoctamerof
int
ermed
iat
efilamentpol
ypep
tid
echai
ns(contai
ns2rowsoftet
ramers
)

B)As
semb
lyr
equi
resac
ces
sor
ypr
otei
ns

-I
F-as
soc
iat
edp
rot
eins(
IFAP’
s)

-Oneexamp
lei
sfi
laggr
in-c
ros
sli
nkedp
rot
ein

4.Maj
orCy
tos
kel
etalFunc
tions
:

A)Sup
por
tsp
las
mamemb
rane

B)Sup
por
tsout
erc
ytop
las
m(c
ort
ex)

C)Sup
por
tst
hei
nnerc
ytop
las
mbet
weent
hec
ort
exandt
henuc
leus

Or
gani
zat
ionofPr
okar
yot
icGenome:

I
.6maj
ord
iff
erenc
esf
romt
heeukar
yot
ic:

1)Pr
okaryot
icgenomes(c
omplet
esetofgenet
ici
nfor
mat
ionor
gani
zedi
ntoac
hromos
ome)ar
emuc
h
smal
lert
haneukaryoti
cgenomes

-E.
col
i-c
irc
ularc
hromos
ome4,
700kb

-Humans
-23l
inearc
hromos
omes3,
000,
000kb

2)I
nbac
ter
iac
irc
ularc
hromos
ome,al
lgenesar
egenet
ical
lyl
inked

-Ther
ear
enot
elomer
es

3)I
npr
okar
yot
es,al
mos
tal
loft
heDNAi
sus
edasgenesorus
edasc
odi
ngs
equenc
es

4)I
npr
okar
yot
es,t
her
eisap
las
midgr
oup
ingoff
unc
tional
lyr
elat
edgenesi
ntoop
erons
5)I
ntr
onsar
eext
remel
yrar
einp
rokar
yot
es

6)Pr
okar
yot
icc
ell
scont
ainext
rac
hromos
omal
piec
esofDNAc
all
edp
las
mid
s

I
I.Ar
rangementofCod
ingSequenc
esi
nPr
okar
yot
es(
oper
ons
):

-mRNAgenesarrangedi
noperons-agrouporcl
usterofst
ruc
tur
algeneswhos
e
coor
dinat
edexp
res s
ioni
scont
r ol
ledbyaregul
atorgene

1.Op
erons
:

A)Op
eronsar
etr
ans
cri
bedasas
ingl
emRNA

B)Ci
str
on-as
egmentofgenet
icnuc
lei
cac
idt
hatc
odesf
oras
pec
ifi
cpol
ypep
tid
echai
n

C)Op
eronsar
econt
rol
ledb
yas
ingl
epr
omot
er,whi
chl
iesi
nfr
ont(
5’)oft
het
rans
cri
beds
egment

-Promoterc
ontai
nsDNA(c
onsensus
)sequenc
est
hatp
rov
ider
ecogni
tion
andbind
ingsit
esforRNApol
ymer
ase

-Regul
atet
her
ateofi
nit
iat
ionoft
rans
cri
pti
on

-I
ndi
cat
ethes
tar
tpoi
ntf
ort
rans
cri
pti
on

2.Pr
omot
ers
equenc
es:

A)2c
ons
ens
uss
equenc
es

1)-10sequenc
eTATATT(Pri
bnowb ox)i
sabout10nuc
leot
idesup
str
eam
(5")fr
omt hestar
tpoi
ntoftrans
cr i
pti
on

2)
-35s
equenc
eTTGACA(
35nuc
leot
idesup
str
eamf
romt
hes
tar
tpoi
ntoft
rans
cri
pti
on

-Thes
etwos
equenc
ess
etab
asalr
atef
ort
rans
cri
pti
on

-Bas
all
evelad
jus
tedb
yregul
ator
ypr
otei
ns(
rep
res
sor
s/ac
tiv
ator
s)

a)Repres
s or
sareregul
ator
ypr
otei
nswhi
chr
educ
ethe
l
eveloftranscr
ipt
ion

b
)Ac ti
vat
or sareregul
ator
ypr
otei
nswhi
chel
evat
ethe
l
eveloftranscr
ipt
ion

3.Examp
leofab
act
eri
alop
eron(
lacop
eron)
-lac
tos
emet
abol
is
m

A)Comp
osedof3genes
:

-z-c
odesf
orb
eta-gal
act
osi
das
e-b
reaksd
ownl
act
oset
ogl
ucos
e&gal
act
ose

-y
-gal
act
osi
dep
ermeas
e
 -a-t
hiogal
act
osi
det
rans
acet
ylas
e

-y&ai
nvol
vedi
npr
otei
ntr
ans
por
t

-Or
gani
zedi
ntop
romot
erandc
odi
ngs
equenc
es

B)Op er
ator-as ec
tionofanop
eroni
nv ol
v edinthecont
roloft hesynthesi
softhegene
productsencodedwithi
ntheoper
on(regionofDNA) ;aregulatorygenethatbi
ndswitha
regulator
yp rotei
nt ot
urnonandof
ft rans c
rip
t i
onofas peci
fiedregi
onofDNA

-Regul
ator
yprot
ein,whi
chbi
ndstotheoperat
orandinhi
bit
sthe
trans
cri
pti
onofstruc
tur
algenes
,iscal
ledarepr
ess
or

-Enc
odedb
yas
epar
ategene

-Inthi
sexampl
eofthelactoseoper
on,ther
eexist
salac
tos
erep
res
sor
,
whic
hbind
st ot
heop
er atorintheabsenc
eoflac
tose

I
I.Lac
tos
eRep
res
sor
:

-Al
sohasab
ind
ings
itef
orl
act
ose

-Whenl
act
osei
spres
ent,wil
lbindtor
epr
essori
nducesaconf
ormati
onalchangeofthe
rep
ress
ormol
ecul
etowhic
hwillnotbi
ndtot
heoperator
,thus,t
ransc
rip
tionwillp
roceed

-Dr
s.Jac
obandMonodf
irs
tdi
scov
eredr
epr
ess
orr
egul
ati
oni
nthe1960’
s

-Followi
ngt ranscr
ipt
ion(pol
yci
stroni
cmes sage-mRNAthatc
odesf
ormorethanone
cis
tr on)
,t r
anslati
onoccur
swher einfor
mat ionofthemRNAisc
onver
tedt
oap ol
ypep
tid
e
chain.(Processedtomatur
ef unct
ionalprot
ei ns

Or
gani
zat
ionofEukar
yot
icGenome:

-Genome-ent
irecol
lecti
onofgenesandal
lot
herf
unc
tionalandnonf
unc
tional
DNA
sequenc
esinthenucleus

I
.Func
tionals
equenc
es:

-Forexamp
le,enc
odemRNA,r
RNA,t
RNA,s
n/s
cRNA’
s

-Rep
lic
ati
onor
igi
ns

-Regul
ator
yel
ementTATACAATb
oxenhanc
ersf
orgeneexp
res
sion

I
I.Nonf
unc
tionals
equenc
es:

-Cons
istofr
epet
iti
ves
equenc
es-DNAs
equenc
es,whi
char
erep
eat
edt
hous
and
sormi
ll
ionsoft
imes

-Ar
rangementoff
unc
tional
;andnonf
unc
tional
sequenc
esar
enotf
ixedi
nthegenome
-Exi
sti
ngs
equenc
eshav
ebeenob
ser
vedt
omov
efr
omonel
ocat
iont
oanot
her=genet
icr
ear
rangement

1.Examp
les
:

-Pr
oduc
tionofi
mmunogl
obul
ins

-Exp
res
sionofmat
inggenesi
nyeas
t

-Exp
res
sionofs
urf
acegl
ycop
rot
einsi
npr
otozoa

I
II.Or
gani
zat
ionDef
ini
ti
ons
:

-Chr
omos
ome-l
inearDNAmol
ecul
e+hi
stones+nonhi
stonep
rot
eins

-Tel
omer
es-endofac
hromos
ome

-Cent
romer
e-hol
ds2c
hromos
omear
mst
oget
her

-Hap
loi
dgenome-c
ont
ainsonec
opyofeac
hchr
omos
ome

-Di
ploi
dgenome-c
ont
ains2c
opi
esofeac
hchr
omos
ome

-Tr
ipl
oid
-cont
ains3c
opi
es(
commoni
npl
ant
s)

-Tet
rap
loi
d-c
ont
ains4c
opi
es(
commoni
npl
ant
s)

-Ps
ued
ogene-nonf
unc
tionalc
opi
esofexp
res
sedgenes

I
V.Or
gani
zat
ionofCod
ingSequenc
es:

1.mRNAgenes

A)80%ofc
odi
ngDNAc
odesf
ormRNA

B)Mos
toc
curi
nsi
ngl
ecop
y(onec
opyp
ergenome)

C)SomemRNAgeneshav
emul
ti
plec
opi
es

-My
osi
n,t
ubul
in,hi
stones
,col
lagens
,Hb
’s,i
mmunogl
obul
ins

2.r
RNA,t
RNA,s
n/s
cRNAgenes

-Exi
stasgenef
ami
li
esi
nmul
ti
plec
opi
es

V.Rep
eti
tiv
eNonc
odi
ngSequenc
es:

-Di
scov
eredi
nthe1960’
sbyDr
s.Br
itt
onandKohne

-Dev
elop
edamet
hodf
ord
etec
tingr
epet
iti
veDNAs
equenc
es=r
eas
soc
iat
ionki
net
ics
1.Undercer
tai
ncond
iti
ons
,theDNAd
oub
lehel
ixwi
llb
reakd
ownt
oar
and
omc
oil
ors
ingl
est
rand
ed
molec
ule

A)Heat

B)Hi
ghp
H

-Bothofthesebr
eaktheHbond sholdi
ngtheb
asepairs
,dis
char
gesthe
hydrop
hobici
nter
acti
onsbetweent hebas
es,per
mit
tingthetwost
rands
toseparat
efromeachother

C)Exp
osur
etoc
hemi
cal
ssuc
hasur
eaord
imet
hyls
ulf
oxi
de

-Thi
spr
oces
sisc
all
edDNAd
enat
urat
ion

-Rev
ers
epr
oces
sofd
enat
urat
ioni
srenat
urat
ionorr
eanneal
ing

-Sinc
er enaturati
onisli
mitedbythefrequenc
yofcol
li
sionof
complementarysequences,therat
eatwhi chi
toc
curswillb
esloweras
thesizeoftheDNAmol eculeinc
reases

-Ex:PCRr
eac
tion

-Mostcommonmethodtomeas
ureDNAd
enat
urat
ioni
sbas
edont
he
hyper
chromi
ceffectofDNA

2.Conc
ept
s:

A)Nuc
lei
cac
idshav
est
rongab
sor
pti
on(
opt
icald
ens
ity
)maxi
maat260nm

-Absorbance(
tur
bid
ityofasolut
ion)
-t hefracti
onofinc
identlight
absorbedbyasol
uti
onatagivenwavelengthandisrel
atedt othe
thi
cknes soft
heabsor
bingl
ayerandthec oncent
rati
onoft heab s
orbi
ng
mol
ec ule

-Ab
sor
banc
eismeas
uredquant
itat
ivel
ybyt
heLamer
t-BeerLaw:l
ogI
o/I
=ec
l

I
o=i
ntens
ityofi
nci
dentl
ight

I=i
ntens
ityoft
rans
mit
tedl
ight

e=mol
arext
inc
tionc
oef
fic
ient(
li
ter
s/mol
e-c
m)

c=c
onc
ent
rat
ionofab
sor
bingmol
ecul
e

l=t
hic
knes
soft
hel
ightab
sor
bings
amp
le

B)Ab
sor
banc
eofd
oub
les
trand
edDNAi
snott
hes
umoft
heab
sor
banc
eforeac
hoft
heb
ases
 -Thehyd
rophob
ici
nter
ac t
ionsandHb ond
ingb
etweent
hes
tuc
kbas
es
reduc
estheOD(ab
sorbance)read
ing

C)Whent heDNAd oublehel

ixisbr
okenordenat
uredt
hes
ef or
cesared
est
royedandthe
opt
icaldensi
tyoft hesolut
ionofDNAisi
ncreas
edbec
auseeachbas
enowcontr
ibut
esit
s
normalopti
caldensit
y

1)I
ncr
eas
einODi
scal
ledt
hehy
per
chr
omi
cef
fec
t:

 -Di
ffer
entDNA’
scanhav
edi
ffer
entmel
ti
ngp
rof
il
es

-Forexample,aDNAmolec
ulethatc
ont
ainsahigh%of
ATb pwi
llhavealowerTmthanaDNAmolecul
ewitha
high%ofGCb p
.

2)Examp
le:

a)HeataDNAs
olut
iont
odenat
ured
oub
lehel
ix

b
)Cool
sol
uti
on10-15’
bel
owt
heTm(
renat
urat
ion)

c)Theseparatedstr
andswil
lcol
li
dewitheac
hotherand
onceinawhilethecomp
lementaryregi
onswil
lfi
ndeach
otherandrenature==doub
lehel
ix

D)Rateofrenat
ur ati
onisli
mit
edb
yther
ateatwhi
chc
oll
is
ionsoc
curb
etween
compl
ement
ar ysequences

sa2ndor 2
1)Thi
si derr
atef
unc
tionb
asedon:r
ate=k[
A][
B]orr
ate=k[
A]

[]=t
hec
onc
ent
rat
ionofs
ingl
ecomp
lement
arys
trand
s(att
imet
)

2)DNAofanor
gani
smi
schar
act
eri
zedb
ythev
alueofCotat½(
50%)r
eas
soc
iat
ion

 -Reas
soc
iat
ionofmammal
ianDNAqui
ted
iff
erentf
romt
heb
act
eri
alDNA(
uni
for
msi
ze)

-Therei
sarap
idl
yreas
soc
iat
ingf
rac
tion=r
epr
esent
srep
eti
tiv
eDNA
sequenc
es

-Thereisamoder
atel
yreas
soc
iat
ingf
rac
tion=r
epr
esentmod
erat
ely
repeateds
equenc
es

-Therei
sasl
owl
yreas
soc
iat
ingf
rac
tion=r
epr
esent
ssi
ngl
ecop
yDNA
sequenc
es

VI
.Ty
pesofRep
eti
tiv
eDNASequenc
es:

1.Mod
erat
elyRep
eat
edSequenc
es(
100-1000)
:

A)Func
tionals
equenc
es:

1)Genec
odi
ngf
orr
RNA,t
RNAandr
epeat
edmRNAgenes
 2)Rep
eat
edgenesatt
het
elomer
es

-Func
tiont
ost
abi
li
zeend
soft
hec
hromos
omes

B)Nonf
unc
tionals
equenc
es

1)Ps
ued
ogene-mut
atednonf
unc
tional
genesar
isi
ngf
romgened
upl
ic
ati
onev
ent
s

2)Cel
ogenes

-Somec
opi
esc
ont
ainaRNAp
oly
mer
aseI
IIp
romot
er

-Ac
tiv
eint
rans
cri
pti
on

-Func
tionofmos
tunknown

2.Hi
ghl
yRep
eat
edSequenc 103t
es( o106)
:

-Hi
ghl
ycons
erv
edwi
thi
nas
pec
ies

-Ac
countf
ort
hel
argec
ont
entofgenomesi
neukar
yot
icc
ell
s

-Ex:s
nai
lshav
emor
eDNAt
hanmammal
s&p
lant
s

-Func
tionoft
hes
equenc
ess
til
lnotund
ers
tood

A)Genet
icr
ear
rangement-DNAs
equenc
esc
anmov
ear
oundwi
thi
nthegenome

-Pr
oduc
tionofant
ibod
ies

-Exp
res
sionofmat
inggenesi
nyeas
t

-Exp
res
sionofs
urf
acegl
ycop
rot
einsi
npr
otozoa

-Ones ourceofgeneticrear
rangementoc
cur
sbytrans
pos
abl
eel
ement
s-
segment sofDNAt hatcanmovefromonepos
iti
oni
nagenometo
another

3.Twoc
las
sesoft
rans
pos
abl
eel
ement
s:

A)Tr
ans p
osons-DNAsequenc
ethatmov
esbyamechani
smt hatc
utsthes
equenc
efr
om
i
tsori
ginall
ocationi
nthegenomeandi
nser
tsi
tinad i
ffer
entsite

-Cont
ainsi
nser
tedr
epeatDNAs
equenc
esateac
hend

B)Retrot
ranspos
on(retr
oposon)-DNAs equencewhic
hdupl
ic
atesandmovest
onew
l
ocati
onsviaanRNAintermediateDNA–t r
anscr
ipti
on RNA--rev
erset
ransc
rip
tas
e
cDNA--"i
ntegr
ase"insertedintogenome

-Rever
setr
ansc
rip
tas
e-enzymef
irstfoundinret
rov
irusesthatmakes
adoubl
est
rand
edDNAc op
yfr
omasingl
e-strand
edRNAt empl
ate
 mol
ecul
e

-Pr
imar
ysour
ceoft
rans
pos
abl
eel
ement
sar
eret
rov
irus
es

-Canb
ehar
mles
sorp
athogeni
c(AI
DS/
canc
er)

DNAr
epai
r/mut
ati
ons
:

-DNAd
oub
lehel
ixi
scons
tant
lyb
eingmod
ifi
ed=DNAd
amage

-Thi
sul
ti
mat
elyc
aus
es80-90%ofhumanc
anc
ers

I
.2Maj
orCl
ass
esofDNADamage:

1.Sp
ont
aneous

A)Sp
ont
aneousDNADamage:

1)Canoc
curv
ia:

a)Er
ror
sinb
ase-p
air
ingd
uri
ngDNAr
epl
ic
ati
on

b
)Er
ror
sinp
roof
read
ing(
3’-5’
exonuc
leas
efunc
tionofDNAp
ol.
)

c
)Er
ror
sinac
ces
sor
ypr
otei
ns(
ex:DNAb
ind
ingp
rot
eins
)

d
)Pos
tDNAr
epl
ic
ati
onmi
smat
cher
ror
s

-Cel
lsel
imi
nat
eDNAd
amage(
les
ionst
hatd
amage)b
ymol
ecul
arDNAr
epai
r

-Fi
rstd
esc
rib
edi
n1945b
yDr
.Kel
ner

-Foundt
hatv
isi
blel
ightp
rot
ect
edmi
croor
gani
smsf
romt
hel
ethalef
fec
tsofUVr
adi
ati
on

2.Env
ironment
al

-Thes
efac
tor
smayov
erl
ap

I
I.Fourd
iff
erentt
ypesofDNAr
epai
rmec
hani
sms
:

1)Di
rec
trep
airofDNA

2)Bas
eexc
isi
onr
epai
r

3)Nuc
leot
ideexc
isi
onr
epai
r

4)Mi
smat
chr
epai
r
1.Di
rec
trep
airofDNA:

A)Ther
ear
e3t
ypes
:

1)Sp
orep
hot
opr
oduc
trep
air

-Res
tri
ctedt
o1s
pec
iesofb
act
eraBac
i il
luss
ubt
il
us

-Rep
air
scy
clob
utaned
imer
sins
por
esandr
equi
resl
ight

2)Phot
oreac
tiv
ati
on

-I
stheenzy
mat
icr
ever
salt
omonomer
sofp
yri
mid
inec
ycl
obut
ane
di
mers

-Di
mersareformedb
ytheUVcomponentofs
unl
ightand
arethemajorc
auseofski
ncanc
er

-Dimer sarer emovedfromDNAb yanenzy mecall

ed
phot ol
iase,whichbind
st othepyrimi
dinedi
merinDNA,
absor bs,ablue-l
ightphoton,andspl
itsthecycl
obut
ane
ri
ngb yelectrontransferfromthephotoexci
tedFADH2
att heac ti
ves i
te(notinhumans )

3)Al
kylt
rans
fer

-DNAal
kyl
ati
onad
duc
ts:

-2majormutantal
kyl
ati
onsi
ghtsonDNAbasesareat
theO6pos
iti
onofguani
neandtheO4pos
iti
onofthymi
ne

-Methy
lgroupsc
anb
eat
tac
hedv
iaav
ari
etyofr
eac
tionsd
uri
ngnor
mal
cel
lmetab
oli
sm

-DuringDNAr epl
ic
ation,theDNAp olymerasewil
lmat
ch
(base-pai)O6met
r hylguaninewitht hymi
ne.IfDNA
mismat chi
snotcorrected
,t heGCb asepairwil
lbe
repl
ac edwithanATb asepair(mutation)
.

-DuringDNAr ep
lic
at i
on,theDNAp olymerasewil
lmat
ch
(base-pai)O4met
r hylthyminewithguanine.IfDNA
mismat chi
snotcorrected,theATb asepairwil
lbe
repl
ac edwithaGCb asepair(mut
at ion)

-Fort
unat el
y,al
lcel
lshaveenzymesthatremovemet
hyl
groupsfromDNA.Themaj orenzymeiscal
ledO6-
methylguani
ne-DNA-methylt
ransfer
ase(MGMT)

-Transf
ersmethyl
groupsfrom06-met
hyl neand04
guani
methylthymi
netoacyst
eineaminoaci
dintheacti
ve
si
teoft heenzy
me
 -Thistrans
ferisani
rrevers
ibl
ereacti
on"s
uici
de
reacti
on"thus;MGMTisnotatrueenzymeperse(nota
cataly
st)

-MGMTf
oundi
nal
lsp
eci
es

-Humanshav
eoneenzy
me

-E.c
olihas2enzymes

-O6methylguaninei
sc y
t ot
oxic
,mutageni
c,and
tumorageni
c ,t
umorc el
lswhic
hlac
kMGMTac ti
vit
yfor
m
tumors.Thi
sMGMTl ikel
yp l
aysasi
gnifi
cantrol
ein
cancerpreventi
on.

2.Bas
eexc
isi
onr
epai
r:

A)ADNAadduct(
modi
fiedordamagedDNAbas
e)isremovedb
yas pec
ialenzy
mec al
l
eda
DNAgl
ycos
ylas
ewhic
hleavesanemp t
ybasesi
te,i
nt heDNAdoub
leheli
x(APsit
e)

B)AP-d
eoxy
rib
osei
sremov
edb
y2enzy
mesc
all
edAPend
onuc
leas
es

-APl
ias
e-enzy
met
hatc
atal
yzest
head
dit
ionoff
unc
tional
group
stod
oub
leb
ond
s

-APhy
drol
ase-enzy
met
hatc
atal
yzeshy
drol
ysi
sreac
tions

C)Themis
singnucl
eoti
deisthenr
epl
acedus
ingaDNAp
oly
mer
aseandt
heDNAd
oub
le
hel
ixi
ssealedt
ogetherus
ingaDNAli
gase

D)Bas
eexc
isi
onr
epai
rsy
stemorr
epai
rst
hef
oll
owi
ngDNAb
asead
duc
t:

1)Ur
aci
l(r
esul
tsf
romt
hed
eami
nat
ionofc
ytos
ine)

2)Hy
droxy
met
hylur
aci
l(oxi
dat
ionoft
hymi
ne)

3)Thy
minegl
ycol
s(d
amagedt
hymi
neexamp
let
hymi
ned
imer
s)

4)8hy
droxy
guani
ne(
oxi
dat
ionp
rod
uctofguani
ne)

3.Nuc
leot
ideexc
isi
onr
epai
r:

-Wor
kst
oget
herwi
thb
aseexc
isi
onr
epai
r

-Remov
esl
argeb
ulkyDNAad
duc
ts

-Ad
duc
tfor
medwi
th:c
isp
lat
in,ni
tros
our
eas
,ni
trogenmus
tar
d=ant
i-c
anc
erd
rugs

A)I
nnuc
leot
ideexc
isi
onr
epai
r:
 1)Amulti
subuni
tATP-d
epend
entnuclease(exc
isi
onnucl
ease,
exc
inuc
lease)makes2cut
sorinc
isi
ons,oneoneithers
ideoftheDNA
add
uct

2)Exc
isesorr
emov
esanol
igonuc
leot
idewhi
chc
ont
ainst
head
duc
t

3)Theexci
sedoli
gonucl
eoti
dei
sthenr
eplac
edbycop
yingt
he
compl
ementaryDNAs t
randusi
ngDNApol
ymeras
e

4)DNAd
oub
lehel
ixi
sthens
eal
edt
oget
herus
ingDNAl
igas
e

4.Mi
smat
chr
epai
r:

A)Bot
hp r
okar
yoticandeukar
yot
icc
ell
sar
ecap
abl
eofr
epai
ringmi
smat
chedDNAb
ase
pai
rsaft
errepl
ic
at i
on

B)Molec
ularmec
hanismsofmismatchrep
airpr
ocess
esar er
elatedt
othemol
ecul
ar
mechani
smsofbaseexci
sionr
ep ai
randnucl
eoti
deexci
sionrepai
r

C)Itisthefunc
tionofthecel
lul
armis
mat chr
epairs
ystemt
orec
ogni
zeDNAbase
mispai
rsandtoeli
minat
ethesebios
ynthet
icmist
akesfr
omnewl
ysynt
hesi
zedDNA
str
ands

D)Mismatchedr
epai
rsyst
emsr el
yonsecond
arysi
gnal
swithint
heDNAd oubl
eheli
xto
id
entifyt
henewlysynt
hesizedDNAs
trand,whi
chbydef
ini
tioncont
ainstherep
lic
ati
on
error
s

E)Signali
sinaGATCsequence;t
headeni
neb
aseismethy
lat
ed(
inp
arent
alGATC
sequence)
;newl
ysynt
hesizedGATCi
snotmethy
lated

1)4p
rot
einsr
ecogni
zedt
hes
ebas
emi
spai
rsonnews
trand(
inc
lud
inganend
onuc
leas
e)

2)Oli
gonucl
eoti
des equence(eit
her3'or5'tothebasemispai
r)is
removedfromthenewl ysynthesi
zedst
rand(thi
sinv
olves3protei
ns-
inc
ludesaheli
case-intr
oducesorremovesDNAsupercoi
ls
)andan
exonucl
ease

3)Ac
orr
ects
trandi
sres
ynt
hes
izedus
ingDNAp
oly
mer
ase

4)DNAd
oub
lehel
ixi
sseal
edt
oget
herus
ingDNAl
igas
e

I
II.Mut
ati
ons
:

-Mut
ati
on-i
stheor
igi
nals
our
ceofgenet
icv
ari
ati
onc
aus
edb
yac
hangei
naDNAb
aseorac
hromos
ome

-Sp
ont
aneousmut
ati
ons
-ist
hos
ethatap
pearwi
thoutexp
lanat
ion

-I
nduc
edmut
ati
ons
-ist
hos
eat
tri
but
edt
oap
art
icul
armut
ageni
c(c
hemi
cal
and/
orp
hys
ical
)agent

-Mut
ati
onsc
anb
eint
rod
ucedi
ntoanor
gani
sm'
sDNAasar
esul
tofunr
epai
redDNAd
amage

-Mut
ati
onsc
anhav
eav
ari
etyofd
ist
inc
tcel
lul
arand
/ormol
ecul
aref
fec
ts
-Al
tert
hes
truc
tur
eofap
rot
ein/
RNA

-Caus
eac
hangei
ngeneexp
res
sion

-Ef
fec
tcanr
angef
romund
etec
tab
let
olet
hal
it
yofanor
gani
sm

1.Mut
ati
onsandmut
ant
s:s
omed
efi
nit
ions
:

-Mut
ati
on-i
saher
itab
lec
hangei
nthes
equenc
eofanor
gani
sm'
sgenome

-Genome-f
ullc
omp
lementofanor
gani
sm'
sgenet
icmat
eri
al

-Mut
ant
-isanor
gani
smt
hatc
arr
iesoneormor
emut
ati
onsi
nit
sgenome

-Gene-b
asi
cuni
tofher
edi
ty

-Al
lel
e-al
ter
nat
efor
mofagene

-Di
ffer
entmutati
onst hatar
el oc
atedatt
hes
amegene(
genet
icl
ocus
)
aresai
dtobeall
elesofeachother

-Loc
us-mapp
ort
ionofagene

-Genot
ype-i
sthegenet
ici
nfor
mat
iont
hatanor
gani
smenc
odesi
nit
sgenome

-Phenot
ype-ob
ser
vab
lec
har
act
eri
sti
csofanor
gani
sm

-Amut
ati
ont
hatasmul
ti
pleef
fec
tsonanor
gani
sm'
sphenot
ypei
ssai
dtob
epl
eiot
rop
hic

-Wil
d-typ
egenotype-r
eferst
ot henormalorpar
ent
alob
ser
vab
lec
har
act
eri
sti
csofan
organi
sm(phenot
ype)(op
erati
onaldef
ini
tion)

-Sc
ient
ist
sus
eas
uper
scr
iptp
luss
ignwhenr
efer
ringt
othewi
ld-t
ypegene(
ex:l
acZ+)

-Amutati
onthatchangest
hep
henot
ypef
romwi
ld-t
ypet
oamut
antgenot
ypei
ssai
dto
beaforwardmutati
on

-Amut
ati
ont
hatc
aus
esc
hangeofgenot
ypef
rommut
antt
owi
ld-t
ypei
ssai
dtob
ear
ever
semut
ati
on

-Mut
ant
scanb
eob
tai
nedb
ysel
ect
ionors
creeni
ng

-Ifacondi
tioncanbearrangedinwhi
challt
hemembersofthepop
ulat
iondieorfai
lto
growexceptforthedes
iredclas
sofmutants,t
hemutantcanbeid
enti
fiedorobt
ained
bysel
ecti
on

-Example:sel
ect
ionforampi
cil
li
nres
ist
antb
act
eri
alc
oloni
es(
or
bacter
ialcell
swhic
hcontai
npUC19)

-Ifi
tisnec
essaryt
oexamineallt
hemember
softhepopulat
iontoid
enti
fythemutant
havi
ngthedes
iredp
henot
ype,themutant
sarei
denti
fiedorobtai
nedbyscr
eeni
ng
 -Amutagenisanagent(c
hemic
al/phys
ical
)(bi
ologi
calvi
rus
est
r ansposab
leel
ement
s)
thatl
eadstoaninc
reaseint
hef r
equencyofoccurrenc
eofmutations

-Thep
roc
essb
ywhi
chmut
ati
onsar
epr
oduc
edi
sref
err
edt
oasmut
agenes
is

-Mutagenes
isthatoc
curswit
houttreat
mentoftheor
gani
smwi
thanexogenous
mutagenisref
erredtoassp
ontaneousmut
agenesi
s

-Thes
emut
ati
onsc
anoc
curb
ecaus
eofr
epl
ic
ati
oner
ror
s

-Occ
urasacons
equenc
eofDNAles
ionst
hatar
eint
rod
ucedi
ntoanor
gani
sm’
sgenome
dur
ingnor
malgrowt
hofthec
ell

-Mutagenesi
sthatres
ultsfromtreatmentofanorgani
smwithac hemic
al,phy
sic
al,or
bi
ologi
calmutageni
sreferr
edt oaschemicalmut
agenes
is;hi
stor
icall
ycall
edUV
mutagenesi
s

-Gener
alt
ermi
sind
ucedmut
agenes
is

-Sp
ontaneousmutat
ionsandi
nduc
edmut
ati
onsc
anb
ethes
ame;t
heyr
efert
ohowt
hey
werei
dentif
iedorob
tained

-I
ft hepresenceofapartic
ularad
d uct(modif
icat
ionorl
esi
on)inDNAcanr
esul
tina
mutati
onatt hesit
ewher etheadductisloc
ated,theDNAadduc
tister
meda
pr
emut ageni
cleson:ex:O6met
i G&O4met T

-Mutati
onsoc
curr
ingatsit
esinDNAwher
ether
ewasnotknownt
obeaDNAad
duc
tar
e
ref
erredtoasunt
argetedmut
ations

-Mut
ati
onf
requenc
y-r
efer
stot
hep
rop
ort
ionofmut
ant
sinap
opul
ati
on

-Mutati
onr ate-expr
essesmutat
ionsgi
vingap art
icul
arobser
vab
lephenotyp
ep erDNA
rep
lic
ation,thiscanbeexpres
sedasmutationsperbasepai
rpercel
ldi
visi
on(repl
ic
ati
on)

-Genomi
cmut
ati
onr
ate-exp
res
sesmut
ati
onsp
ergenomep
erDNAr
epl
ic
ati
on(
cel
ldi
vis
ion)

2.Twoc
las
sesofmut
ati
ons
-di
ffer
entt
ypesofmut
ati
ons
:

A)Simp l
emutati
ons(p
ointmutat
ions)-aremutat
ionsthatresul
tfr
omthesubs
t i
tut
ion
of1b asepai
rforanotherorf
romt headd
iti
onordelet
ionofoneorasmal
lnumberof
basep ai
rs

-Mos
tcommonl
yres
ult
sorar
isef
romexp
osur
est
ophy
sic
alorc
hemi
cal
mut
agen

B)Comp
lexmut
ati
ons
-inv
olv
eext
ens
ivec
hangesi
nDNAs
truc
tur
e

1)Del
eti
on-isamut
ati
onwhichi
nvol
vesalossofoneormor
ebas
epai
rs;
whereachromos
omals
egmentorgeneismis
sing

2)Inser
tion-amutat
ionwhichinv
olvest
headdi
tionofgenet
icmat
eri
al;
whereac hromos
omalsegmentorgenesaread
ded
 3)Dup
lic
ati
on-s
ituat
ioni
nwhi
chac
hromos
omal
segmentorgenei
srep
eat
ed

-Li
nked
-tand
emd
upl
ic
ati
on

-Ornotl
inked

4)I
nver
sion-al
ter
ati
oni
ngenes
equenc
einac
hromos
ome

-Per
icent
rici
nver
sioni
ncl
udest
hec
ent
romer
e

-Par
acent
rici
nver
siond
oesnot

-Furthermore,fororganis
mst hathav e>1c hromosome,
mutationaleventscanoccurthati nv
olvet hejoi
ningof
theDNAofonec hromosometot heDNAofanot her,
therebycausingac hr
omosomalr earrangement( ex:a
transl
ocation-movementofac hr omosomes egment
fromonec hromosomet oanot
herc hr
omos ome)

3.Ty
pesofp
ointmut
ati
ons
:

A)Bas
esub
sti
tut
ionmut
ati
ons
-res
ultf
romt
hes
ubs
tit
uti
onofoneb
asep
airf
oranot
her

1)Trans
iti
onmutat
ion-amutat
ionthatinvol
vesac
hangef
romone
puri
neforanot
heroronepy
rimi
dineforanother

GC ATAT GC

2)Trans
fusi
onmutati
on-amutati
onthati
nvol
vestheint
erchangeofa
puri
neforapyr
imi
dineorthei
nter
changeofapyri
midi
neforap ur
ine

GC TAGC CGAT TAAT CG

B)Mi
ssensemutati
ons-isbas
esub
sti
tut
ionmut
ati
onst
hatc
hanget
hec
odonf
orone
ami
noacidtothatforanot
herami
noaci
d

1)Ef
fec
tsofmi
ssens
emut
ati
ons
:

a)Nod
etec
tab
leef
fec
t

b
)Par
tiall
ossoff
unc
tion

c
)Gai
noff
unc
tion

d
)Al
ter
ati
onoff
unc
tion

e)Changei
npr
otei
nst
abi
li
ty

-Temp
erat
ureef
fec
t

-p
Hef
fec
t
 f
)Comp
let
elos
soff
unc
tion

C)Sil
entorneutr
almut
ati
ons-iswhenabas
esubs
tit
uti
onmutat
ionc
hangesac
odon
fromoneaminoaci
dtoadi
ffer
entcodonf
orthes
ameaminoac
id

-Duet
othed
egener
acyoft
hegenet
icc
ode

D)Nonsens
emutati
ons
-ismut
ati
onst
hatc
hanget
hec
odonf
oranami
noac
idt
ooneof
thethr
ees t
opc
odons

-TAG,TAA,TGA=us
ual
lyl
eadt
ocomp
let
eorp
art
iall
ossoff
unc
tionoft
hegenep
rod
uct

-Phenotyp
icef
fec
tsofnonsens
emutati
onscanb
eal
ter
edors
upp
res
sed
byas ec
ondmutat
ion=nons
ensesup
presser

-Nonsensesuppresser
-isamutat
ionoccur
ringwit
hinageneencodinga
tRNAandal t
erst heanti
cod
onofthatt
RNAs othatitc
anr ec
ognizea
nonsensecodon

-Inac el
lthatcontai
nsanons ensemut ati
onandanons ensesuppres
ser,
whent henonsensecodonisread,atleastaf rac
tionofthetimethe
aminoacidcarri
edbyt henonsensesuppressertRNAisinser
tedintothe
growingpolyp
eptid
ec hai
n

-Pr
event
schai
nter
minat
ion

-Pr
otei
nfunc
tional

-Phenotyp
eoft hemutantorganis
miswild-t
y p
eev enthoughits
genotyp
ed if
fersfr
omt hatofitswil
d-ty
pep arentbythepresenceof
boththenonsensecod
onandt henonsensesuppressermutati
ons

E)Ad
dit
ion/
Del
eti
onofb
asep
air
s:

-Frames
hiftmutati
ons-mutat
ionst
hatal
terors
hif
tthet
rans
lat
ional
readi
ngframe(notingroup
sof3)

Canc
er:

I
.Int
rod
uct
ion:

-Canceristheleadi
ngcaus
eofd eathforwomenintheU.
S.-d
uet
othec
ons
ist
ent
decl
ineinheartdis
easemortal
it
yi nthel
ast40year
s

-Canc
erwi
llb
ethel
ead
ingc
aus
eofd
eat
hint
heU.
S.b
ythey
ear2000.

-Mos
tcommonc
anc
ersar
ecaus
edb
ytob
acc
oandal
cohol

1.Cancer
-amalignanttumorr
esul
ti
ngfromap r
ogressi
veseri
esofgeneti
candcell
ularev
ent
swhi
ch
occuri
nas i
ngl
ec l
oneofcel
lsd
uetoalt
erati
onsinali
mitednumberofspec
ifi
cgenes

A)Onc
ogenes
B)Tumors
upp
res
sergenes

C)Tumors
usc
ept
ibi
li
tygenes

-Canc
er,ortheprocessofc
arc
inogenes
is,c
anb
edi
vid
edi
nto2ormor
est
agesd
epend
ing
onthetypeofcancer

-Ini
tiati
on-i
saclonalexpansi
onofcel
lsthatgai
nas el
ect
ivead
vant
ageb
ygenet
ic
changesinthec
ells(mutati
ons)pr
e-canc
er ouss
tat
e

-Promot
ion(
progr
ess
ion)
-whent
her
eisanac
cumul
ati
onofgenet
ical
ter
ati
onsi
nthes
epr
e-c
anc
erous
cel
ls

-Thes
ealter
ati
onsar
ec aus
edbyini
tialgenet
icchangesandcanals
ooc
curb
yexp
osur
e
ofthecel
lstot
umorpromoti
ngcompoundssuchasphorboles
ters

-Thes
eal
ter
ati
onsc
aus
ethep
henot
ypeoft
hes
ecel
lst
ochangei
ntomor
emal
ignant
ones

-Measur
ementofage-depend
entcancerss
uggestthatatl
east2ormorethan7
ind
ependentev
ent
sar enecess
aryforthedev
elopmentofmal
ignantt
umor
s

I
I.Ther
ear
etwot
ypesoft
umor
s:

1)Beni
gn(
pri
mar
yorp
remal
ignant
)tumor
sar
egr
owt
hs,whi
chr
emai
nconf
inedt
oit
snor
mall
ocat
ion

-Ex:war
ts

2)Mal
ignant(c
ancer
ous
)tumor
sar
egr
owt
hst
hatc
ani
nvad
enon-t
umor
oust
iss
uesv
iat
hec
irc
ulat
ory
orl
ymphatics
ystems

-Mov
ementofc
anc
eroust
umor
stonon-t
umort
iss
uesi
scal
ledmet
ast
asi
s

-Mor
et han100di
ffer
entkind
sofhumanc anc
ersar
erec
ogni
zedandhi
stor
ical
ly
cl
ass
ifi
edaccord
ingtothei
rcell
ularor
igi
n.

I
II.Mos
tcanc
ersar
edi
vid
edi
nto5maj
orgr
oup
s

1)Car
cinomas

2)Sar
comas

3)Leukemi
as/
lymp
homas

4)Car
cinomas
:

-Comp
ris
eap
proxi
mat
ely90%ofhumanc
anc
ers

-Ar
isef
romep
ithel
ialc
ell
s

5)Sar
comas
,leukemi
as,l
ymp
homas
:
 -Sarcomasarecanc
ersofconnect
ivetiss
ueormusc
letis
sue;d
evel
opf
rommes
oder
mal
cel
lsand/orc
irc
ulator
ycel
lsofthebloodandl
ymphsys
tem

-Leukemi
asar
ecanc
ersd
eri
vedf
romhemop
oiet
icc
ell
s(b
loodb
onemar
rowc
ell
s)

-Ly
mphomasar
ecanc
ersd
eri
vedf
roml
ymp
hcel
ls

-Tumor
sar
efur
therc
las
sif
iedt
othei
rti
ssueofor
igi
n

-I
samul
ti
stepp
athwayt
hatl
ead
stoc
olonc
anc
er

-Thi
spat
hwayi
ncl
udes5genes
:

-p
53,DDC,APC,r
ask

-Inthi
spathwayther
emustbeatleas
t7ind
epend
entgeneti
cev
ents(
2eachforp53,
DDC,andAPCandoneforr
ask)foranormal
cel
ltochanget
oametast
ati
ctumor

-Ithasb eenknownf ors

ever
alyearst
hatchangesi
nDNAandnotchangesinother
subcel
lul
arc omponentss
uchasl
ipi
dsandpr
oteinsar
eres
ponsi
blef
ort heformati
onof
canceroustumor s

-Tr
ans
geni
cmous
ecel
lsc
hangedi
ntot
umorc
ell
s

-Itwasf urthers hownt hattheDNAinthehumancancercell

sc ont
ainedanac
tivat
ed
oncogene,whic hwasnotp r
esentinthenon-t
umormous ecel
ls.However,t
hetransgeni
c
tumormous ec ell
sc ont
ainedtheacti
vatedhumanoncogene

I
II.Chr
omos
omalr
ear
rangement
s

-Manygenet i
cchanges,whi c
hleadtocancer,arelargechromosomalrear
rangements
thatarevisi
bleund ertheli
ghtmicr
oscope.Humanc hromosomescanbep r
eparedin
cultur
ep l
ates/t
ub esandtherearespeci
ficbondi
ngp atternsthatar
euniquet oeach
chromosomeandt hesep at
ternsaregenetic
all
yinherited

-Chromosomalaberrati
ons(genet
icrearrangements),whi
chleadtocancer
,canbe
transl
ocatedbetweenchromosomes,del
etionofallorpartofachromosomeoran
inver
sionwithi
nac hromosomeorothermor ecomplexrearr
angements

-Thus,amolecul
archarac
ter i
zati
onofchr
omosomalr
earr
angementas
soc
iat
edwi
th
cancershoul
dleadt
ot heidenti
fic
ati
onofgenesi
nvol
vedi
ncancer

-Thi
smol
ecul
archaract
erizat
ionhasl
eadtot
hecloni
ngofDNAsequenc
esats
pec
ifi
c
part
sofhumanc
hr omosomeswhic
hareass
oci
atedwithc
ancerand

-Amol
ecul
armapoft
hehumangenomei
sbei
ngc
ons
truc
tedus
ingov
erl
app
ingDNAf
ragment
s

-Iti
simpor
tanttod
eter
minewhichDNAsequencesar
er espons
ibl
efort
he
tr
ansfor
mationf
romnormalc
ell
stometastati
ctumorcell
s

-Burki
tt’sl
ymphoma.I
nthi
scaset
hereisareci
proc
altr
ansl
ocat
ionbet
ween
chromosome8and14andpl
acesaprot
o-onc
ogenenexttoanAbgene
 -Thi
sev
entc
aus
est
heac
tiv
ati
onofap
rot
o-onc
ogenet
oanonc
ogene

I
V.Onc
ogenes
:

1.Ear
ly1980’
sDr
.Bi
shopd
isc
over
edonc
ogenes
:

A)Genet
hatc
aus
esat
umor

B)Fi
rstd
isc
over
edi
nret
rov
irus
es(
rasgene)

C)Prod
uctofanoncogeneisrequir
edf orthet
r ansf
ormi
ngac
tiv
ityoft
hev
irus(
abi
li
ty
ofthevir
ustochangenormalcel
lsint
ot umorcell
s)

D)Onc
ogeneac
tinad
omi
nantmanner

-Het
erozy
got
eist
umor
ageni
c

-Studi
esononcogenesi
nthe1980’
sledtot
hedis
cov
er ythatt
hehos
t
cel
lhasaninac
tiveformoftheonc
ogene(p
rot
o-oncogene)

2.Pr
oto-onc
ogene:

A)Cel
lul
arc
ount
erp
artoft
heonc
ogene

B)Notexp
res
sedi
nthec
ellorexp
res
sedatl
owl
evel
srel
ati
vet
otheac
tiv
atedv
iralonc
ogene

C)Cel
lul
arp
rot
o-onc
ogenec
anb
eac
tiv
atedt
oanonc
ogeneb
ymut
ati
on

D)Mut
ati
onalev
entc
anb
eas
imp
leb
ases
ubs
tit
uti
onoramor
ecomp
lexc
hromos
omal
rear
rangement

E)Pr
oduc
tsofonc
ogenesar
ecal
ledonc
opr
otei
ns;t
hes
epr
otei
nsc
arr
youtav
ari
etyofc
ell
ularf
unc
tions
:

1)Protei
nt y
r osi
neki
nases-enzymet hatphos
phoryl
atest
yros
ine
resi
dues-involv
edinsi
gnaltrans
d uc
tionpathways

2)Gr
owt
hfac
tor
s-s
ignalmol
ecul
est
hatar
einv
olv
edi
nregul
ator
ycel
lgr
owt
h

3)Gprotei
ns-heter
otri
mer
icGTP-b
ind
ingp
rot
einst
hatar
einv
olv
edi
n
si
gnaltr
ansducti
onpat
hways

4)Tr
ans
cri
pti
onf
act
ors
-pr
otei
nst
hatf
unc
tioni
nmod
ulat
inggeneexp
res
sion

-Morethanthree-d
ozent
umorv i
ruseshavebeenident
ifi
edandthi
sisali
stof29
retr
ovirus
es,t
henameoft hei
rtransfor
mingoncogeneandthei
roncop
rotei
ngene
produc
t

-Onc
ogenessuchasr
asH,raf
,jun,andfosc
anf unc
tioninsignalt
rans
duc
tionp
athway
s
whereachemic
alorphy
sic
alsi
gnali
srec
ognizedbythecell

-Thec
ellwi
llev
ent
ual
lys
tar
tpr
oduc
ingas
pec
ifi
csetofp
rot
einsi
nres
pons
etot
he
si
gnal
3.Si
gnalt
rans
duc
tionp
athwayus
inganonc
ogene:

A)Relayi
ngofasi
gnalbyconver
sionf
romonep hy
sicalorchemic
altoanot
her
;the
proc
es sb
ywhic
hac el
lconver
tsanextrac
ell
ulars
ignalint
oar espons
e

1)Gr
owt
hfac
torb
ind
stoar
ecep
tor

2)Bi
ndi
ngac
tiv
atesat
yros
inep
rot
einki
nas
e

3)Ac
tiv
atesRas

4)Rasacti
vates,insequence,3cytopl
asmi
cprot
einki
nases:Raf
,MEK
(mi
togenextracel
lul
ar-s i
gnal
-regul
atedki
nas
e),MAPK(mit
ogen
act
ivati
ngproteinki
nas es)

-Ser
ine/
thr
eoni
nep
rot
einki
nas
esc
all
edi
ntr
acel
lul
art
rans
duc
ers

-MAPKap rot
einki
nas ethatp er
formsac r
uc i
alstepi
n
relayi
ngs i
gnalsf
romt hep l
asmamemb ranet othe
nuc l
eus.Ki
naseactivatedbyawi derangeof
proli
ferati
onord i
fferenti
ationinduci
ngsignals

5)Ac
tiv
ationofMAPK(p
hos
phoryl
ati
on)all
owstheki
nas
et omov
efr
om
thec
ytopl
asmthrought
henucl
earenvel
opeint
othenucl
eus

6)MAPKt
henac
tiv
atesJunandEl
kI(
trans
cri
pti
onf
act
ors
)byp
hos
phor
ylat
ion

7)JunandEl
kIwil
lbi
ndtothepr
omoter
sofj unandf
osgenes
resp
ecti
vel
yandt
hese2geneswi
llb
eexpres
sed

8)Andb
egintop
roduc
ejunandfosmRNAwhi
chwi
llt
henb
etr
ans
por
ted
outtothecy
topl
asmwher
ethe

9)Mes
sages(
mRNA)wi
llb
etr
ans
lat
edt
oJunandFosp
rot
eins

10)JunandFoswil
lbi
ndtoget
hertoforma(heter
odi
mer
s)
transcr
ipt
ional
acti
vati
ngcompl
ex(AP-1c
omplex)

11)AP-1compl
exwil
lbetransport
edf
romt
hec
ytop
las
mthr
ought
he
nucl
earenvel
opetothenucleus

12)AP-1complexwil
lact
ivat
eanumberoft
argetgenes(??)w,whic
h
l
eadstocellt
ransformati
on,ort
hec
onvers
ionofnormalcel
lstot
umor
cel
ls

-Theearl
ys tep
sint hi
ss i
gnaltrans d
ucti
onpathwayhavebeeneluc
idatedingreatdetai
l,
buttheactualmechanismsofc el
lulartr
ansf
ormationwhic
har i
sesfromt heexpres
sion
ofhostcel
ltargetgenesiss t
il
lp oorl
yunder
stood.

4.Tumors
upp
res
sergenes
:

A)5f
eat
uresoft
umors
upp
res
sergenes
:
 1)Incontr
as ttoi
nacti
vecel
lul
arpr
oto-oncogenes,tumors
uppress
er
genesarehighl
yacti
veinnor
malcel
lsandtheyf unct
iontorep
resscel
l
growth

2)Inact
ivat
ionofat
umors
upp
res
sergeneb
ymut
ati
onl
ead
stoad
eregul
ati
onof
cel
lul
argrowth

3)Canc
er s
,whichareformedduetot
heinacti
vat
ionoft
umor
supp
ressergenes,ar
einheri
tedinadomi
nantfas
hion

4)However,tumors
upp
res
sergenesac
tinar
eces
siv
emanner(
het
erozy
got
eisnon
tumorageni
c)

5)Foll
owinginac
tivat
ionofthefi
rstall
eleb
ymutation,t
hechromosome
contai
ningthesecond,andonl
yotherwil
dtypeal
lel
eisusual
lyl
ost

-Pr
oces
sofc
hromos
omal
los
sisc
all
edl
ossofhet
erozy
gos
ity(
LOH)

B)Humanc
anc
er:

1)p
53-isthemostc
ommontar
getofmut
ati
onsi
nhumanc
anc
er(
p53
mutat
ionsarei
n>50%ofcancer
oust
umors
)

a)Cel
lul
arp53-appear
st or
egulatecel
ldiv
isi
onand
mutat
ionsi
nt hi
sgeneleadtoderegul
atedcel
lgrowt
h

-Hasa"
hots
pot
"forG Tt
rans
ver
sions(
benzop
yrene)

b)Mutat
ionsintheRB1geneareass
oci
atedwithret
inob
las
toma-
humanchil
dhooddi
seas
eandinv
olv
estheformat
ionofatumoronthe
reti
na

c
)Mut
ati
onsi
ntheDDCgenear
eas
soc
iat
edwi
thc
olonc
anc
er

-Therecessivenatureoftumors uppress
ergenesc anb evisuali
zedthroughthe
const
ructionofc el
lhybri
ds.I
nt hisexperi
ment,nor malcell
sar efusedwithtumorcel
ls
thatcontainamut ati
oninat umors uppr
essergene.Ther es ult
ingcel
lhybri
disnon-
tumoragenic.Thisres
ultdemonstratesthatthewild-t yp
eal lel
e(formofthegene)from
thenormalc el
lissuff
ici
enttores toreanormal(nont umorageni c
)phenotyp
e

-Cel
lhy
bri
dsar
ety
pic
all
yuns
tab
le

-I
fthewi
ld-t
ypet
umors
upp
res
sergenei
slos
t,t
hehy
bri
dcel
list
rans
for
medb
ackt
oat
umorc
ell

-Ret
inob
las
toma,whi
chi
scaus
edb
ythei
nac
tiv
ati
onofat
umors
upp
res
sergene,RB1

-Thi
sdi
seas
eisi
nher
itedi
nanaut
osomal
(nots
ex-l
inked
)domi
nantmanner

5.Theaut
osomald
omi
nanc
e

A)Af
terinac
tiv
ati
onofonetumors up
pres
s erall
elebymutat
ion,thesec
ondal
lel
eis
i
nacti
vat
edbyanon-di
sjunc
tional
,eventduringmitos
iswherethechr
omosome
 c
ont
aini
ngthewil
d-t
yp etumorsupp
resseral
lel
eislostandt
hec
hromos
omet
hat
c
ont
ainsthemut
ant(inac
t i
vated
)all
elei
sdupli
cated

-Nond
isj
unc
tion-d
efi
nedasanab
nor
mals
epar
ati
onofc
hromos
omesi
nmi
tos
is(
mei
osi
s)

B)Thi
spr
oces
sist
ermedl
ossofhet
erozy
gos
ity(
LOH)

C)LOHc anb
ed et
ectedb
yac hangeofgeneexp
ressi
onofcl
osel
yli
nkedl
ociandbythe
absenc
eofc hr
omosomalDNAsequenc
esthatarel
inkedt
othetumorsup
pressergenes

-Indi
vidual
swhohav eaf amil
yhist
oryofcancers
,whichareass
ociat
ed
withtumors up
pres
s ergenes,aremoreli
kel
yt odev
elopcanc
ersthan
indi
vid
ualsthathavenohi s
toryoffamil
ycancers

-I
nher ed
ityc
ancerassociat
edwit
htumorsup
pres
sergenes
,thef
irs
t
mutat
ionisal
readypr
es entint
heger
mline

-Thi
sind
ivi
dualonl
yneed
stoacqui
reasec
onds
omat
icmut
ati
ont
hatwi
ll
l
eadtotheformati
onofacanc
eroust
umor.

-Howev
er,i
nspor
ad i
ccanc
ers,thedev
elopmentofatumorrequi
resat
l
east2somati
cmutati
oneventsint
het umorsupp
res
sergene.

-Thus,onecanseethatindi
vid
ualswhoalreadycarryamutantformofa
tumorsuppres
sergenear emuchmorelikel
ytod ev
elopcanc
ersinc
eonly
onesomaticmutati
on,ratherthantwo,isneededfortumorfor
mat i
on.

-Kar
yot
ype-ap
hot
ogr
aphi
corp
ict
ori
alr
epr
esent
ati
onoft
hec
hromos
omesi
nagi
veni
ndi
vid
ual

-RB1isrec
es s
ivei
nnatureb
ecausei
fawi
ld-t
ypeRB1genei
sint
rod
ucedi
ntoa
reti
nobl
astomatumor(
transv
ecti
on)
?

-Tr
ans
fec
tion-i
ntr
oduc
tionofDNAi
ntoanon-b
act
eri
alc
ellt
her
esul
ti
ngc
ell
isnon-t
umor
ageni
c

6.Tumors
usc
ept
ibi
li
tygenes
:

A)Genesd
onotac
tiv
elyc
aus
ecanc
er

B)Mut
ati
ons(
inac
tiv
ati
on)i
nthes
egenesl
eadt
oani
ncr
eas
edi
nci
dentofc
anc
er

C)Sev
eraloft
hes
egenesar
eas
soc
iat
edi
nDNAr
epai
r

-Examp
lesd
efec
tinDNAl
igas
e,met
hyl
trans
fer
ase

-Withtheid
entifi
c ati
onoftumorsuscep
tibi
li
tygenes
,stud
ieshaveshownaninter
action
betweenoncogenes ,t
umorsuppres
sergenes,DNArepai
rgenes,andgenesi
nvol
vedin
regul
atingthecellcycl
e(cel
lcy
clegenes)

-Acti
vat
ionofatumorsupp
ress
ergene(p53)andanoncogene(
p21)af
tert
hec
ell
has
beenexpos
edtoagent
s(ex:UVrad
iati
on)thatcandamageDNA.

-Thep
rod
uct
soft
hes
egenesc
ani
nter
actwi
thc
ell
ularp
rot
einst
oar
res
tthec
ell
pri
or
 t
omi
tot
icd
ivi
sion(
inor
dert
orep
airDNAd
amage)
.

-Thecel
lhassensorymechani
sms(p
53/
p 21)
,whic
hcani
nter
rup
tnor
malc
ell
div
isi
onunt
il
genet
icandsubcell
ulard
amagecanberepai
red

7.Themol
ecul
arc
har
act
eri
zat
ionofc
anc
ergenesandd
evel
opmentofnewp
ros
pec
tst
opr
eventand
treatc
ancer

A)Mol
ecul
art
echni
quesc
anb
eus
edt
oid
ent
ifyi
ndi
vid
ual
swi
thi
nher
iteds
usc
ept
ibi
li
tiest
ocanc
er

-Thes
etec
hni
quesc
oul
drel
iab
lyd
etec
tear
lyp
re-mal
ignants
tages

B)Thedev
elop
mentofdi
agnos
ticap
pli
cat
ionsf
ort
heanal
ysi
sofonc
ogeneshasal
read
y
beenus
edincli
nic
alp
rac
tic
e

-Abnormalit
iesofoncogeneshavep r
ovid
edusefulassays(det
ecti
on
method)formonitori
ngt hecourseofthedis
eased uri
ngtreatment
(ampli
fic
ationbyPCRofanonc ogenefusi
onevent( b
cr/ab
l)todetec
t
l
eukemiac ell
s

C)Thed
evel
opmentofd
rugst
hatt
argetagai
nstonc
ogenes

-Forexamp
le,t
hefus
ionofaret
anoi
cacidrec
eptortoanonc
ogene
l
eadstooneformofl
eukemi
aifyout
reatthepat
ientwit
hretanoi
cac
id
(RA)

-RAwi
llb
indt
otheRAr
ecep
torandt
hisb
ind
ingwi
llp
rev
entac
tiv
ati
onoft
heonc
ogene

-Whenpat
ientswi
ththi
stypeofl
eukemi
aaretr
eatedwi
thRA
treat
mentlead
s(>90%)tor
emiss
ionofthet
umor

Tr
ans
cri
pti
onFac
tor
s:

-Structuralmoti
fs(st
ruct
urald
esign)(
famil
ies)foundintr
anscri
pti
onfactor
s-
auxi
liar
yp rotei
ns(bey
ondthe8to14d i
sti
nctp ol
ypepti
desthatmakeupthepoly
mer
ases
)
thatassis
ti ntheop
erati
onofeukaryoti
cpolymerases

I
.Leuc
inezi
pper
-isas
tret
chofami
noac
idsr
ichi
nleuc
iner
esi
duest
hatp
rov
idead
imer
izat
ionmot
if

-Leuc
inezi
pperp
rot
einsc
anf
ormd
imer
sthr
oughahy
drop
hob
ici
nter
fac
e

-Di
merf
ormat
ionr
equi
redf
orDNAb
ind
ing

-c
-jun/
c-f
os=l
euc
inezi
pperp
rot
eins

-Het
erod
imer
s-zi
pper
edp
air
sofnoni
dent
icalp
rot
eins(
usedt
otur
not
hergenes"
on"
/"of
f")

-Heter
odi
mersofc -Jun/
c -Fosoncopr
otei
nsb
indDNAmuc
hmor
est
rongl
ythan
homodi
mersofc-Fosorc -Junalone
II
.Heli
x-l
oop-hel
ix(
HLHprot
ein)-afamil
yofp r
otei
nsi
nwhi
chap
ort
ionoft
hep
oly
pep
tid
efor
ms2al
pha
-hel
ic
esseparatedb
yaloop(theHLHdomain)

-Thi
sdomai
nac
tsasas
equenc
e-s
pec
ifi
cDNA-b
ind
ingd
omai
n

-c
-my
cenc
odesaHLHt
rans
cri
pti
onf
act
ors

I
II.Zi
ncf
ingerp
rot
ein-hasar
epeat
edmot
ifofami
noac
ids(
ric
hinc
ytos
ine/
his
tid
ine)t
hatb
indt
oZn

-p
rot
einc
anb
indt
oDNAand
/orRNAf
ormszi
ncf
inger
s

I
V.heli
x-turn-hel
ix-ahi
ghl
ycons
erv
edf
ami
lyofs
equenc
es(
60ami
noac
ids
/180b
p’s
)(homeob
ox)i
n,
l
engt
h( homeodomain)

-b
indDNAi
nas
equenc
e-s
pec
ifi
cmanner

-hel
ix3=i
sther
ecogni
tionhel
ixandmakesi
mpor
tantc
ont
act
swi
thDNA

-hel
ic
es1&2=makesc
ont
actwi
thot
herp
rot
eins

Rec
omb
inantDNAt
echnol
ogy
:

-enabl
esindivi
dualf r
agmentsofDNAfromanygenometob
einser
tedi
ntovect
orDNA
molec
ules(e.g.pl
as mids
,vi
ruses
)andthesefr
agmentsc
anbeintr
oduc
edintobac
ter
ia
(e.
g.transformation)andthenampl
if
ied

-d
onoror
gani
sm-or
gani
smund
ers
tud
ythatd
onat
esDNA

-ex:f
rui
tfyDr
l osophi
lamel
anogas
ter

-v
ect
orDNAmol
ecul
es-p
las
mid
s/v
irus
est
hatc
anac
cep
tfor
eignDNAs
equenc
es;c
apab
leofr
epl
ic
ati
ng

-t
rans
for
mat
ion-i
ntr
oduc
tionofv
ect
orDNA(
plas
midDNA)i
ntoab
act
eri
alc
ell

-t
rans
fec
tion-i
ntr
oduc
tionofav
irusi
ntoahos
tcel
l

-ex:i
ntr
oduc
ingl
amb
dab
act
eri
ophage(
vir
ust
hati
nfec
tsb
act
eri
a)i
ntob
act
eri
alc
ell
s

-r
ecomb
inantDNA(
chi
mer
icDNA;af
terGr
eekmons
terChi
mer
a)-v
ect
ormol
ecul
e+DNAi
nser
t

-r
ecomb
inant(
DNA)c
lone-al
argep
opul
ati
onofi
dent
icalDNAi
nser
ts

I
.St
epsi
npr
oduc
ingRec
omb
inantDNAmol
ecul
es:

1)I
sol
ati
ngDNA-b
othd
onorandv
ect
orDNA

-d
onorDNAi
sol
atedb
y"genomi
cpr
ep"p
roc
edur
es

-v
ect
orDNA:
 1)p
las
midal
soi
sol
atedus
ingav
ari
etyofp
roc
edur
es"
mini
","
mid
i","
maxi
"pr
eps

2)
vir
usesc
anal
sob
epur
ifi
edus
ing"
phagep
rep
s"

2)Cut
tingDNA:

-exonuc
leases
-c l
eavenuc
leot
idesoneatat i
mefromtheendofap
oly
nuc
leot
idec
hai
n;
theymayb espec
ifi
cforei
ther5’or3’endofDNAorRNA

-end
onuc
leas
es-c
leav
ebond
swi
thi
nanuc
lei
cac
idc
hai
n

-res
tric
tionenzy
mes-endonuc
leas
esthatrecogni
zes
peci
fics
hor
tsequenc
esof(
usual
ly
)
unmethyl
atedDNAandcl
eavethedoub
le-st
randedmol
ecul
e

-produc
edb
ybac
ter
iaasad
efens
emec
hani
smagai
nstp
hages(
par
toft
her
est
ric
tion/
mod
ifi
cat
ion
sy
st em)

-enzy
mesc
utDNAi
ntof
ragment
sofas
izes
uit
abl
eforc
loni
ng

-enzymesc
anmake"st
aggered
"cuts
,whi c
hgener
ates
ingl
e-s
trand
ed"
sti
cky
"end
s
conduci
vet
othefor
mationofrec
ombinantDNA

-mos
tr es
tri
cti
onenzy
meseitherr
ecogni
zeas
pec
ifi
c4b
p"f
ourc
utt
ers
"oras
pec
ifi
c
6bp"
sixcutt
ers"DNAs
equenc
e

-"
4cut
ter
s"wi
llc
utonc
e,onav
erage,ev
ery44b
ases=256b
ases

-"
6cut
ter
s"wi
llc
utonc
eev
ery46b
ases=4096b
ases

-2examp
lesofr
est
ric
tionenzy
mes
:

-namedaf
tert
heor
gani
smf
romwhi
chi
twasi
dent
ifi
edorp
uri
fiedf
rom

1)Ec
oR1-f
romb
act
erumEs
i cher
ichi
acol
i

2)Hi
ndI
II-f
romb
act
erumHaemop
i hil
usi
nfl
uenzae

-b
othar
e6c
utt
ers

-Ec
oR1=r
ecogni
zesa6b
ppal
ind
romes
equenc
e

-b
othDNAstr
and
shav
ethes
amenuc
leot
ides
equenc
ebuti
nant
ipar
all
el
or
ient
ati
on

5’
-GAATTC-3’
=>5’
-GAATTC-3’
3’-CTTAAG-5’
=>3’
-CTTAAG-5’

-s
tagger
edc
ut-l
eav
esap
airofi
dent
icals
ingl
e-s
trand
ed"
sti
ckyend
s"

-end
scanHb
ondt
oac
omp
lement
arys
equenc
e

3)Joi
ningDNA:
-d
onorDNA(
for
eignDNA)+v
ect
orDNA=d
iges
tedwi
thr
est
ric
tionenzy
me/
mixed=>r
ecomb
inantDNA

-j
oinf
ragment
s(v
iaHb
ond
ingofc
omp
lement
arys
equenc
es)
(anneal
ing)
;cat
aly
zedb
yenzy
meDNAl
igas
e

-s
eal
sni
ckst
hathav
eav
ail
abl
e3’
-OHand5"
-PO4t
ermi
ni

-us
esATPasanener
gys
our
ce

4)Amp
lif
yingr
ecomb
inantDNA:

-r
ecomb
inantp
las
midDNAi
sint
rod
ucedi
ntohos
tcel
lsb
ytr
ans
for
mat
ion

-v
ect
orwi
llr
epl
ic
ate(
donorDNAwi
llal
sor
epl
ic
ate)

-wi
llhav
emul
ti
plec
opi
esofv
ect
ori
ncel
l

-c
ellwi
llal
sor
epl
ic
ate(
cel
ldi
vis
ion)

-f
r o109c
om1t ell
s/ml

I
I.Cl
oni
ngas
pec
ifi
cgene:

1.Choos
ingac
loni
ngv
ect
or:

-mus
tbes
mal
l(f
ormani
pul
ati
on/
conv
eni
enc
e)

-mus
tbeab
let
orep
lic
ate

-mus
tcont
ainc
onv
eni
entr
est
ric
tions
ites

-mus
tbeab
let
oid
ent
ify
/rec
overr
ecomb
inantmol
ecul
es

2.Cl
oni
ngv
ect
ors
:

A)Pl
asmi
ds:

-aut
onomous
,sel
f-r
epl
ic
ati
ng,ext
rac
hromos
omal
cir
cul
arDNA

-d
ist
inc
tfr
omb
act
eri
alc
hromos
omes

-1stp
las
midt
hatwasi
dent
ifi
edwast
heFp
las
mid

1)ep
isome-c
anexi
sti
n2f
orms

a)
sel
f-r
epl
ic
ati
ng

b
)int
egr
ati
oni
ntoc
hromos
ome

-sexpl
asmidinvol
vedi
nb ac
teri
alconj
ugati
on-theunionof2bac
ter
ial
cel
ls,dur
ingwhichchr
omosomalmateri
ali
stransf
erredfromt
he
donor(
Hfr)tothereci
pient
(F-)cel
l
  

2)examp
lesofp
las
mid
s:

a)p
BR322-c
ont
ains2d
rugr
esi
stanc
egenes

1)t
ctR=t
etr
acy
cli
ner
esi
stanc
e

-tetr acycl
ine-bi
nd sto
ap rot ei
nont he30S
subuni toft heri
bosome
andi nhibi
tsr i
bosomal
trans loc
ation

2)amp
R=amp
ici
ll
inr
esi
stanc
e

-amp i
cil
li
n-inhi
bits
enzymet hatare
invol
vedinthe
synthesi
soft hecel
l
wall

-bl
a-c od
esforan
enzymethatissecret
ed
tocell
wallandbreaks
downamp

-donorDNAc anbe
inser
tedintotct
Rgene
=inserti
onal
inact
ivati
on

-s
elec
tfort
ctS/
amp
Rcol
oni
es

b
)pUCp
las
mid
s:

1)plasmid
shaveamut ati
onina
rep
licati
ongene(ropgene)whi
chl
ead
s
toincreasedc
opynumb er

2)hasap
oly
cloni
ngs
ite(
pol
yl
inker
;mul
ti
plec
loni
ngs
ite)

-aDNAs equencethat
wasgenet i
cal
ly
construc
tedinvitroand
contai
nsmanys it
es ,
whicharerecogni
zedb y
restri
cti
on
endonucl
eases

3)poly
linkerins
erted(i
nserti
onasi
n-
framewi thB-galcod
ingsequenc
e)i
n
thelacZgene( B-gal
actosi
dase)
 -vectorc ontai
nsDNA
sequenceenc odi
ngt he
1st146ami noacidsofB-
galactosi
d as
e,thus,
pUCv ectorsexpressthe
NH2t erminalofB-
galactosi
d as
e

4)rec
ipi
entcel
ls(
e.g.DH5al
pha)exp
res
stheCOOH
ter
minalfr
agment

5)ac
tiv
eB-gal
act
osi
das
epr
otei
nisahomot
etr
amer

-multi
meri
cenzy me
witheachpol
ypepti
de
consi
sti
ngof1173
aminoaci
dsinlengt
h

6)the2f r
agment swill t
henj oin
togetherint ranstof ormaf unc t
ional
genep roduct(parti
alp roteinsc odedb y
2fragment suni t
etof ormaf unctional
B-galpr ot
ein)=c al
ledal pha-
complement at
ion

7)t
hus
,onec
and
etec
tlac
Zexp
res
sion(
B-galac
tiv
ity
)

A)vect
or+c el
ls(
e.g.DH5al
pha)
(lac
-)
=>B-galac
tivi
ty(l
ac+)

-B-galac ti
v i
tyi nthe
presenc eofac olorless
sub s
t rat ecall
edX-GAL
(5-br omo-4-c hlero-3-
indoy l
-B-D-gal ac t
os i
de)
willpr oduceac olored
(chromogeni c-produces
ac olor edpi
gment )(
b l
ue)
produc t

B)vec
tor+i
nser
t+c ell
s=>noB-gal
act
ivi
ty=whi
tecol
onies

-col
ony-av
isi
blec
lone
ofcel
ls

8)ins
ertionofaf ragmentofforeign
DNAintot hep ol
ycl
oni ngsi
teofpUC
resul
tsinp roducti
onofanami no-
termi
nalf ragmentt hatisnotcapabl
eof
alp
ha-comp lementation

9)p
UCp
las
mid
sus
ual
lyac
cep
tfor
eignDNAupt
o10kb
3.Bac
ter
iop
hage:

-v
irus
est
hati
nfec
tbac
ter
ia

A)l
amb
da-c
onv
eni
entc
loni
ngv
ect
or

1)
acc
ept
sfor
eignDNAus
ual
ly10-15kb

2)
cent
ralp
ort
ionofp
hagegenomenotr
equi
redf
orr
epl
ic
ati
onp
ackagi
ng

-c
anb
eremov
edus
ingr
est
ric
tionenzy
me

3)
lamb
dac
anb
eamp
lif
iedt
ogetl
argeamount
soff
orei
gnDNA

B)c
loni
ngi
nlamb
da:

1)nones
sent
ialr
egi
onofgenomed
isc
ard
ed(
leav
ingl
eft
/ri
ghtar
ms)

2)f
orei
gnDNAd
iges
tedi
nto10-15kbf
ragment
s

3)forei
gnDNAli
gat
edintoar
ms(endsofarmsconnec
tedt ofor
mal ong
l
inearmolec
ulec
onsi
sti
ngofmul
ti
plephagegenomes(conc
atenatedDNA)

-c
onc
atemer
-ser
iesofuni
tgenomesr
epeat
edi
ntand
em

4)DNAt henp
lac
edi
ntoav
iralhead(
cap
sid=c
omp
osedofv
iralp
rot
eins
)inv
itr
o
packagi
ng

C)Cos
mid
s:

-hy
bri
dvec
tor
sofl
amb
dap
hages+p
las
mid
s

-c
anr
epl
ic
atei
nac
elll
ikeap
las
midorb
epac
kagedl
ikeap
hage

-c
osmid
scanacceptfor
eignDNAupt
o45kb(
reas
ont
hatmos
toft
he
l
ambdagenomehasbeendel
eted
)

-however
,cos
mid
sst
il
lcont
aint
hes
ignals
equenc
est
hatp
romot
ephagehead
stuf
fing
(cossi
tes
)

-shuttl
ev ector
s-isap l
asmidcons
tructedtohaveori
ginsforDNA
repl
icati
onf or2hosts(E.col
i/
S.cerevis
iae)sot
hatitcanb eusedt
o
carryforeignsequencesi
neitherprokaryot
esoreukaryot
es

D)Si
ngl
e-s
trand
edp
hages(
M13)
:

-us
efuli
nDNAs
equenc
ing

-expres
sionv
ect
ors
-wher
ecl
onedgenesc
anb
etr
ans
cri
bedandt
rans
lat
edi
ntoa
prot
ein
 -op
enreadi
ngframe(ORF)
-aDNAs
equenc
ethatc
anb
econv
ert
edt
oan
ami
noacids
equence(
viaRNA)

-cansynt
hesi
zeaforei
gnprotei
ninabacter
ialcel
l(remember
,bac
ter
ia
cannotpr
oces
sint
rons=thus,cl
onecannotcont
ainintrons
)

I
II.YAC’
s-y
eas
tar
tif
ici
alc
hromos
omes
:

-f
orei
gnDNA+y
eas
tcent
romer
esequenc
es+y
eas
ttel
omer
esequenc
es

-c
anb
eas
semb
ledi
ntoar
tif
ici
alc
hromos
omes(
upt
o1000kb
)

-YAC’
sus
eyeas
tcel
lsashos
ts

I
V.BAC’
s-b
act
eri
alar
tif
ici
alc
hromos
omes
:

-b
asedonFf
act
or(
sexf
act
or)

-ac
cep
tupt
o300kb(
usual
ly100kb
)

-onead
vant
ageofBAC’
sov
erYAC’
sist
hatoneus
esb
act
eri
alc
ell
srat
hert
hany
eas
tcel
ls

V.Cl
oni
ng/
cons
truc
tingaDNAl
ibr
ary
:

-s
our
ceoff
orei
gnDNA

-l
ibr
ary
-isas
etofc
lonedf
ragment
stoget
herr
epr
esent
ingt
heent
iregenome

-"s
hotgun"c
loni
ng-exp
eriment
erc l
ones(i
solates
)al
argesampl
eofDNAf
ragment
s
hopi
ngthatoneofthecl
oneswil
lcontai
na" hit
"thed
esi
redgene

1.Di
ffer
entt
ypesofl
ibr
ari
es:

A)b
asedon:

1)t
ypeofv
ect
or

2)s
our
ceofDNA

3)d
iff
erentc
loni
ngv
ect
orsc
arr
ydi
ffer
entamount
sofDNA

4)c
hoi
ceofv
ect
ord
epend
sons
izeofgenome

a)s
mal
lgenomes=p
las
mid
s/p
hages

b
)mi
ddl
egenomes=c
osmi
ds

c
)lar
ges
tgenomes=YAC’
s/BAC’
s
B)genomi
cli
brar
y-c
ont
ainsent
iregenome(
int
rons
,exons
,et
c.)

C)cDNAl
ibr
ary(c
ompl
ement
aryDNA)-i
ssynthet
icDNAmadef
rommRNA(catal
yzedbyan
enzymec
all
edrev
ers
etrans
cri
ptas
e-ori
ginal
lyi
sol
atedf
romret
rov
irus(
tumorvirus
)

mRNA–r
ever
set
rans
cri
ptas
e s
sDNA–DNAp
ol d
sDNA

-thus,forexamp l
e,ifascient
istknowsthatap art
icul
argeneishi
ghl
y
expressed(i
.e.thereisl
otsofp rot
ein)i
nap ar
t i
culart
issueofan
organis
m,t henonec anconstruc
tac DNAli
braryusingthemRNAf r
om
thattissue

2.Us
ingPr
obest
ois
olat
esp
eci
ficc
lones
:

32 3
-prob
e-anuclei
cac
idmolec
ulet
hatc
anb
edet
ect
edb
yrad
ioac
tiv
e( P/H)met
hod
sor
chemil
umi
nes
centmethod
s

-pr
obesdep endonthenaturaltendencyofonesi
ngle-s
trandofnuclei
c
aci
dtof i
ndandb as
e-pair(hybr
idize)t
oac ompl
ementarybasesequence
vi
aHb onding

A)Wher
edoesp
rob
ecomef
rom?

1)y
ouc
ans
ynt
hes
izei
t

2)y
ouc
angeti
tfr
omaf
riend"
cloneb
yphone"

3.Cl
oni
ngSt
eps
:

A)tr
ansf
ercol
onies/
p l
aques-cont
aini
ngforeignDNAofi
nteres
tf or
mt hepetrid
ishes
tomemb
ranefi
lterscomposedofni
troc
ell
ulos
eorny l
on=col
onyli
fts/pl
aqueli
fts

-DNAmus
tbed
enat
uredonf
il
ter
sof
tenb
ychemi
cal
treat
ment(
e.g.NaOH)

B)b
athmemb
ranewi
ths
olut
ionc
ont
aini
ngp
rob
e

-p
rob
emus
tbed
enat
uredf
irs
t-heati
t

C)r
emov
epr
obe/d
evel
opf
il
ter
stod
etec
tpr
esenc
eofc
omp
lement
aryDNAs
equenc
es

-Sout
hernbl
otti
ng(DNA-DNAhybri
dizat
ion)
-d es
crib
estheproc
edur
efortrans
ferr i
ng
denat
uredDNAfromanagarosegeltoanitroc
ell
ulosef
il
terwherei
tcanb
ehy bri
dized
withacompl
ementar
ynuclei
caci
d

-res
tri
cti
ond
iges
tsofgenomi
cDNAp
rod
ucesawi
dear
rayofDNAf
ragment
sdi
ffer
ingi
n
si
ze

-wi
lll
ookl
ikeas
mearonanagar
osegel

-ap
rob
ecand
etec
tas
pec
ifi
cDNAr
est
ric
tionf
ragment

1)s
epar
ated
iges
tedgenomi
cDNAus
ingagar
osegelel
ect
rop
hor
ies
is(
gel
 f
rac
tionat
ion)
(DNAf
rac
tionat
ion)

2)l
ayab
sor
bentmemb
rane(
nit
roc
ell
ulos
e/ny
lon)
ont
opoft
hegel

-DNAtrans
ferred/"
blotted"fr
omgelt
omemb r
anesb
y
capi
ll
aryac
tion(DNAs t
ay sinthes
amepos
iti
on)

3)exp
osememb
ranet
oap
rob
eofi
nter
est(
rad
ioac
tiv
epr
obe)

4)r
emov
epr
obeandl
ayap
hot
ogr
aphi
cfi
lmov
ermemb
rane

-exp
oseandd
evel
opf
il
m

-wi
lls
eeas
pec
ifi
cbandont
hisf
il
m

-Autorad
iogr
aphy-pr
ocesst
hatdet
ectsr
adi
oac
tiv
elyl
abel
edmol
ecul
esb
ythei
ref
fec
tin
creati
nganimageonphot
ograp
hicfi
lm

-Sout
her
nbl
ott
ing=DNA-DNAhy
bri
dizat
ion

-Nor
ther
nbl
ott
ing=DNA-RNAhy
bri
dizat
ion

-Wes
ter
nbl
ott
ing=p
rot
ein-ABi
nter
act
ions

4.Fi
ndi
ngs
pec
ifi
ccl
onesb
yfunc
tional
comp
lement
ati
on:

-cl
onedgenescanb
ed et
ect
edt
hrought
hei
rab
ili
tyt
oconf
erami
ssi
ngf
unc
tionona
tr
ansformati
onrec
ipi
ent

-ec
top
icexp
res
sion-d
esc
rib
est
heexp
res
sionofagenei
nat
iss
uei
nwhi
chi
tisnotus
ual
lyexp
res
sed

-ectop
ici
nsert
ion-ins
erti
onofrecomb
inantDNA(vect
or+ins
ert
)int
oar
eci
pient
’s
genomeatalocati
onthati
sdif
ferentfromit
sori
ginalsi
te

-pos
itionalc
loni
ng-anymethodthatusesinf
ormat
ionab
outagene’
sloc
ati
onorp
osi
tion
onac hromosomeinor
dertoisol
atethatgene

-chromosomewal
king-desc
ribesthesequenti
alisolat
ionofcl
onesc
ar ryi
ngoverl
app
ing
sequencesofDNAall
owingl
argeregionsofthec hromosometobespanned.Wal
kingi
s
oftenperfor
medinordertoreachap art
icul
arlocusofinter
est

A)Cloni
ngaGeneb yTaggi
ng-canisolat
easpec
ifi
cgeneb
yind
uci
ngamut
ati
oni
nthat
gene(i
nser
tionalmut
agen=transp
os abl
eel
ement)

1)P-el
ement-c
l nDr
onegenesi osophi
la

2)Ty
1el
ement-c
lonegenesi
nyeas
t

Cel
lul
arr
epr
oduc
tion:
-ac
cor
dingt
ocel
ltheor
y,newc
ell
sor
igi
nat
efr
omot
herl
ivi
ngc
ell
s

-p
roc
ess=c
elld
ivi
si
on=c
ell
ularr
epr
oduc
tion

-mot
her
(par
ent
al)c
ell d
aught
er(
off
spr
ing)c
ell

I
.Rev
iewc
ellc
ycl
e:

1.Cont
rolofc
ellc
ycl
e(2c
ont
rolev
ent
sinc
ellc
ycl
e):

A)i
nit
iat
ionofDNAr
epl
ic
ati
onwhi
choc
cur
satt
het
rans
iti
onb
etweenG1/
S

B)i
nit
iat
ionofmi
tos
iswhi
choc
cur
satt
het
rans
iti
onb
etweenG2/
M

-r
es ear
chonfactor
scontrol
li
ngt
hec
ell
cyc
leb
egani
nyeas
twi
tht
he
di
scoveryofagenecal
ledc
d c
2

-b
udd
ingy tSac
eas char
omyc
esc
erev
isi
ae

-f
iss
iony tSc
eas hizos
acc
har
omyc
espomb
e

-r
eveal
edal
arge#ofgeneswhos
epr
oduc
tsf
unc
tiont
omai
ntai
nthep
rop
erc
ell
cyc
le

-werei
denti
fied(>80genesid
entif
ied)asc ondi
tionalmutati
ons(
ts=
temp
eratur
es ensi
tiv
e)call
edcdcmutations(cel
lc yc
ledi
visi
on)

-wi
llgr
ownor
mal
lyatl
owt
emp
s(p
ermi
ssi
vet
emp-23’
C)

-wi
lls
topgr
owi
ngathi
ghert
emp(
res
tri
cti
vet
emp36’
C)

-apar
ticul
arcdcmut antwi
llst
opgrowingataspeci
fict
imeint
hec
ell
cyc
le(
allcel
lswi
llexhibi
tasimi
larmorp
hologi
cal
phenotype)

-inc
ontrastt
oat ypi
calt
smutati
on,cel
lwi
lls
topatv
ary
ingp
oint
sin
thecel
lcyc
le(numer
ousphenot
ypes)

C)rest
rict
ion("
start
")p
oint-d
uri
ngt
heG1p
has
eoft
hec
ell
cyc
le,t
hep
ointatwhi
ch
thecel
liscommi
ttedtod
ivi
de

1)f
act
orsi
nfl
uenc
ingr
est
ric
tionp
oint
:

a)c
ells
ize-r
ati
oofc
ytop
las
micv
olumet
ogenomi
csi
ze

b
)r egul
ator
ypr
otei
ns-f
unc
tionasamol
ecul
arc
loc
ktoc
arr
youtt
he
c
ellcycl
e

-t
ypesofr
egul
ator
ypr
otei
ns:

A)prot
einkinases-an
enzymethatregulates
theacti
vit
yofanot her
 protein,ortarget
molecule,byaddinga
PO4d erivedf
romATP

B)c y
c l
in-dependent
kinases( Cdk’
s)-a
proteint hatisacti
ve
onlywhenat tachedtoa
particularcycli
n

C)cycl
ins -proteins
whosec oncent rati
on
fluc
tuat esovert ime
(amountofp r otei
n
vari
esinac ycle=
peri
odicf l
uctuat i
ons)

2.entryi
ntoMphase(mi
toti
cphas
e)tri
gger
edbytheacti
vat
ionofa
protei
nki
nasec
alledmat
urati
on-pr
omoti
ngfac
tor(MPF)

a)MPFc
ont
ains2s
ubuni
ts:

1)
cat
aly
tics
ubuni
tATP ADP+PO4(
ser
/thr
)

2)
regul
ator
ysub
uni
t=c
ycl
in

--fi
rstyeastc
d cmutat
ion=c d
c S.
2(
pombe)/
cdc28(S.cer
evi
siae)

-whenmut
ated
,cel
lst
opsgr
owi
ngat:

1)ei
therjustpri
orto
DNAr ep
lic
ationor

2)
jus
tpr
iort
omi
tos
is

-p
rod
uctofc
dc2i
scat
aly
ticuni
tofMPF

-cdc2regul
at edatend
ofG1andatendof
G2(det
er mi
nedb y
temperature-shi
ft
experi
ment)

-bothc el
lcycl
es tages
representpointsint he
cel
l cyc
lewhenac ell
becomesc ommittedt o
beginningcruci
al events

a)
DNAr
epl
ic
ati
on

b
)nuc
leard
ivi
sion
 -passaget hr
ought hese
pointsrequir
est he
transientacti
vat i
onof
Cdk’sbys p
ecifi
cc ycl
ins

-passaget hrough
START( G1/ Srestr
ict
ion
point)requiresthe
activ
ationofc dc2bya
G1c ycl
in(cig2)

D)cd
c2cig2di
mer-p ass
agethrought
hes ec
ondpointofc
ommitmentj
ustbefor
et heend
ofG2requi
resac
tiv
at i
onofc
d c
2b yadif
ferentgroupofcy
cli
ns(mi
tot
iccy
cli
ns)(
cdc13)

E)cdc
2cdc13di
mer-Pr
ogres
sionthroughthecel
lcy
cler
equi
rest
hep
hos
phor
ylat
ionand
dep
hopsp
horyl
ati
onofc
ert
ainc r
iti
calaminoac
ids

-pr
iortomitosi
s(G2/
Mc heckp
oint
)-Cdksubunitmustb
ep hosphor
ylat
ed
atthreoni
ne-161=cataly
zedbyCAK(Cdk-acti
vati
ngkinase)

-t
her
eisal
sop
hos
phor
ylat
ionatt
hreoni
ne14/
tyr
osi
ne15=c
atal
yzedb
ywee1andmi
k1

-t
hisi
nhi
bit
sCAKac
tiv
ity

-ac
tiv
ewee1ormi
k1p
rod
ucesani
nac
tiv
ecd
c2c
dc13enzy
mec
omp
lex

-t
yros
ine15/
thr
eoni
ne14PO4’
scanb
eremov
edb
yap
hos
phat
asec
dc25

-thus
,thecdc
25p hos
phataseandwee1/
mik1ki
nas
esac tascompeti
tors
tooneanot
her,onestimul
atingcd
c2andtheot
herinhi
bit
ingitsac
tivi
ty

I
I.p
rot
einki
nas
es/
cont
rolofc
elld
ivi
sion:

1)t
hec
ycl
ini
ssy
nthes
izedt
hroughoutt
hec
ycl
eandac
cumul
atesd
uri
ngi
nter
phas
e

2)Cy
cli
nat
tac
hest
oCd
k(c
dc2)andt
hep
rot
einc
omp
lexi
sac
tiv
atedatt
heendofi
nter
phas
e

3)Theac
tiv
ecompl
ex,MPF(matur
ationp r
omotingfac
t or
),coor
dinat
esmi
tos
isb
yphos
phor
ylat
ing
vari
ousp
rotei
nst
hatincl
udepr
oteinkinasesp
hos p
hatases

4)Oneoft
hep
rot
einsac
tiv
atedb
yMPFi
sac
ycl
ind
egr
adi
ngenzy
met
hatd
est
roy
sMPFac
tiv
ity

5)TheCdkcomponentofMPFi
srecyc
led
,it
ski
nas
eac
tiv
ityr
est
oredb
yas
soc
iat
ionwi
thanewc
ycl
in
thatac
cumulat
esd ur
ingi
nter
phas
e

Cy
top
las
micMemb
raneSy
stem:

-i
nter
nalc
ytop
las
mics
truc
tur
esf
irs
tob
ser
vedb
ybi
ologi
stsi
nthe1940’
swi
tht
he
 d
evel
opmentoftheel
ectronmi
cros
cop
es(
sci
ent
ist
ssawmemb
rane-b
oundv
esi
cl
esof
v
aryi
ngelec
trondens
iti
es

-el
ect
ronmi
cros
cop
esp
ort
rays
tat
ic,notd
ynami
cpr
oces
ses

-c
ist
ernae-f
lat
tenedmemb
rane-b
oundc
omp
art
ment

-c
ytop
las
mofeukar
yot
icc
ell
ssub
div
idedi
ntoav
ari
etyofd
ist
inc
tcomp
art
ment
s(b
ound
edb
ymemb
ranes
)

-endomemb ranes y
s t
em-f uncti
onal
lyandstr
uctural
lyi
nter
relatedgroupof
memb ranouscytoplasmi
corganell
esi
ncludi
ngtheendopl
asmi
cr et
icul
um,Golgic
omp l
ex,
endosomes,lysosomes,andvacuol
es(nucl
earenvel
opecanbeincl
uded-notac ytop
lasmi
c
organell
e)

-transp
ortves
icl
es-theshut
tles,formedb
ybud
dingf
romamemb
ranec
omp
art
ment
,
thatcarrymat
erial
sbet
weenor ganel
les

-bud
dingfi
ssi
oncycl
e-v es
icl
esmov
ethroughthecyt
opl
asmi
nad
irec
tedmanneron
tr
acks(cy
toskel
etonthenfuset
othenextcompar
tment

I
.Di
sti
nctc
ytop
las
micp
athway
s:

1.biosyntheti
cp athway( secretoryp athway)-r outethr
oughthec ytopl
asmbywhi chmaterialsare
synthesizedintheend op l
asmicreticulumorGol gicompl
ex,modi
fiedd uri
ngpassaget hr
ought heGolgi
comp l
ex,andt r
ans portedwi t
hint hec ytopl
asmt ovari
ousdesti
nationssuchast heplasmamemb r
ane,
l
y s
os ome,oralar gevac uole(pl
antc ell
)( al
ter
nat etermsecr
etoryp athwayhasb eenusedbec ausemany
ofthemat er
ial
ss ynthes i
zedint hepat hwayared esti
nedtobedischargedouts
id ethecel
l)

-t
hisi
ncl
udest
hef
lowofl
ipi
ds,c
arb
ohy
drat
es,andp
rot
eins

A)2t
ypesofs
ecr
etor
ypat
hway
s:

1)consti
tuti
vesecr
et i
on-disc
hargeofmaterialss
ynthesi
zedinthecel
l
int
ot heextrac
ell
ularinaconti
nued,unr
egulatedmanner(contr
ibut
es
tof or
mat i
onofpl
as mamembrane/ext
racel
lul
armat r
ix)

2)regulatedsecretion-di
schargeofmat er
ialssynthesizedi
nthecel
l
thathav ebeens toredi
nmemb rane-boundsecret
or ygranulesi
nthe
peripheralregi
onsoft hecytop
lasm,occurri
nginr esponsetoan
appropriatesti
mul us

-produc
t i
on/r
eleaseofhor
mones
,di
ges
tiv
eenzy
mes
,or
neurotransmi
tters

2.Endoc
yticpathway-rout
eformovi
ngmateri
alsfromoutsi
dethecel
l(andfromthemembranesur
fac
e
ofthecell
)tocompart
ments,s
uchasend
osomes(ex:ly
sosomes)
,loc
atedwithi
nthecel
lint
erior

-t
rans
por
trequi
rest
raf
ficp
att
erns
:

ex:s
ali
var
y s
ecr
etor
yves
icl
esd
iges
tiv
eenzy
mes l
ysos
omes

-p
rot
einsar
etar
get
edt
hroughs
ort
ings
ignal
s-r
ecogni
zedb
yrec
ept
orsi
nthewal
lsoft
rans
por
t
v
esi
cl
es

I
I.St
udyofCy
tomemb
ranes
:

1)Aut or adiography( hi
stori
c al)-at echniquef orvisual
izi
ngb iochemicalprocessesbyall
owingan
inves t
igat ortod eterminet hel oc
at i
onofr adioactiv
elylabeledmat eri
alswi t
hinac el
l.Ti
ssues ec
tions
cont ainingr ad
ioac ti
veisotop esarec overedwi that hi
nlayerofp hot
ograp hi
cemul si
on,whichisexposed
byr adiat i
onemanat i
ngf romt hetissue.Sitesinthec el
l-containingradioactiv
ityarerevealedunderthe
micros copeb ys i
lvergrainsaf terd evel
opmentoft heoverlyi
ngemul s
ion

2)pulse-chas eexperi
ments-arep erf
ormedb yi
ncubat i
ngcel
lsv
erybri
efl
y(pul
se)wi
thar ad
ioact
ivel
y
l
abeledp r
ec ursor(ofsomepathwayormac romolec
ule);thent
hefateofthel
abeli
sfol
lowedduri
nga
sub
s equenti ncubati
onwithanonlabel
ed(chase)precursor

3)cellfracti
onati
on-s ep ar
ationofv esic
lesderiv
edf r
omf us
ionoft
heendsofmemb r
anefragment
s
thatf or
mup onhomogeni zati
onofc el
ls
.Vesic
lesf or
medf r
omeachofthedi
fferentmembr
anous
organell
es(nuclei
,mitoc hondria,plasmamemb rane,endopl
asmicr
eti
cul
a,et
c.)havedi
ffer
ent
bioc
hemi cal
/physi
calp
r op erti
est hatall
owt hi
ss eparat
ion

-e.
g.c
ytop
las
m-(
homogeni
zat
ion)
fr
agment f
usei
ntov
esi
cl
es

-mi
cros
omes-aheter
ogeneouscoll
ect
ionofsimil
ar-si
zedvesi
cl
esformedfr
omt
he
end
omembranes
yst
em( p
rimari
lytheendopl
asmicreti
culumorGol
gicompl
ex)

4)Us
eofmut
ant
s(y
eas
t)-Dr
.Rand
ySc
hel
man

-i
sol
ati
onofs
ecr
etor
ydef
ect
ivemut
ant
s(c
lonedgenes
;anal
yzedgenep
rod
uct
ssuc
has
pr
otei
ns)

-r
eveal
edt
hatc
omp
onent
sofend
omemb
ranes
yst
em

-highl
yconserved(yeas
t,p
lant
s,humanhav
esi
mil
ars
ecr
etor
ypr
otei
ns)(
canc
orr
ect
yeastdefec
t swithmammali
angene)

End
opl
asmi
cRet
icul
um(
ER)
:

-r
oughER-at
tac
hedr
ibos
omes

-s
moot
hER-nor
ibos
omes

I
.fl
uidofc
ytop
las
m-d
ivi
dedb
yERi
nto2c
omp
art
ment
s:

1)l
umi
nal(
cis
ter
nal
)sp
ace-s
pac
ebet
weenERmemb
ranes

2)c
ytos
oli
csp
ace-r
egi
onout
sid
eERmemb
ranes

-r
ibos
omesf
acec
ytos
oli
csp
ace
I
I.Smoot
hER(
SER)-p
res
enti
nskel
etalmus
cle,ki
dneyt
ubul
es,s
ter
oid
-pr
oduc
ingend
ocr
inegl
and
s

1.Func
tions
:

A)s
ynt
hes
isofs
ter
oidhor
monesi
ntheend
ocr
inec
ell
soft
hegonad
/ad
renalc
ort
ex

B)d
etoxi
fic
ati
on(
li
ver
)

-oxy
genas
es(
P450s
yst
em)-c
onv
ert
shy
drop
hob
icmol
ecul
est
ohy
drop
hil
icmol
ecul
es

-b
enzop
yrene BPDE(
car
cinogen)

C)c
onv
ert
sgl
ucos
e-6-PO4 gl
ucos
e(l
iver
)

-al
lowsgl
ucos
etob
erel
eas
edi
ntot
heb
lood
str
eam

D)s
eques
t sCa++-c
er anb
eus
edi
nav
ari
etyofc
ell
ularr
eac
tions

I
II.RoughER:

1.Func
tions
:

A)s
iteofs
ynt
hes
isofs
ecr
etor
ypr
otei
ns

B)s
ecr
etor
ypr
otei
nsc
ont
ainas
ignals
equenc
eatN-t
ermi
nus(
6-20nonp
olarami
noac
ids
)

C)tr
iggersatt
ac hmentofrib
os ometoERmemb
rane/
mov
ementofnas
centp
oly
pep
tid
e
i
ntocist
ernalspace(si
gnalhypothes
is)

1)mRNAt
rans
lat
edi
ntop
oly
pep
tid
eonf
reer
ibos
ome(
w/s
ignals
equenc
e)

2)s
ignals
equenc
erec
ogni
zedb
ysi
gnalr
ecogni
tionp
art
icl
e(SRP)

-6p
oly
pep
tid
es

-75LRNA(
scRNA)

-s
top
str
ans
lat
ion/
prot
einf
old
ing

3)SRP+p
oly
pep
tid
e=SRPc
omp
lexb
ind
stoERr
ecep
toront
hec
ytos
oli
csi
deofER

-t
rans
lat
iont
henp
roc
eed
s

4)SRPr
eleas
ed(
requi
resener
gyGTP)(
Gpr
otei
ns)(
sec
ondmes
sengerp
athway
s)

-p
oly
pep
tid
eent
ersc
ist
ernae(
trans
loc
ati
on)

5)s
ignals
equenc
eisr
emov
edus
ings
ignalp
ept
idas
e

6)ad
dit
ionofol
igos
acc
har
ides(
oli
gos
acc
har
ylt
rans
fer
ase)
 7)p
rot
einp
rop
erl
yfol
ded(
usess
pec
ial
izedenzy
mese.
g.d
isul
fi
dei
somer
ase)

2.Gl
ycos
ylat
ors
:

N-l
inkagest
oas
par
agi
ne

O-l
inkagest
oser
ine/
thr
eoni
ne

-ad
dit
ionofsugarst
oagr owi
ngoli
gosacc
hari
dechai
nc atal
yzedb
ygl
ycos
ylt
rans
fer
ases
-enzymesthattr
ansferamonos
acchari
detoasugarreceptor

A)Gol
gic
omp
lex-1898Cami
ll
oGol
gi-Nob
elPr
ize(
1906)

1)Networkofs moothmembranesorganizedi
ntoachar
acter
ist
ic
morphol
ogy,cons i
sti
ngoffl
attened,di
sl
ikeci
ster
naewithdi
lat
edri
ms
andassoci
atedv esi
cl
esandtubules

2)Gol
gic
ist
ernaear
epol
ari
zed
:

-c
ist
ernaec
los
estt
oER=c
isf
ace

-op
pos
itec
ist
ernae=t
ransf
ace

3)Gol
gic
omp
lex-p
roc
ess
ingp
lant
,mod
ifi
cat
ionofp
rot
eins

-d
ivi
dedi
nto4f
unc
tional
lyd
ist
inc
tcomp
art
ment
s:

1)
cisc
ist
ernae

2)
med
ialc
ist
ernae

3)
transc
ist
ernae

4)
transGol
giNet
wor
k(TGN)

4)Pas
sageofmol
ecul
esf
romERt
hroughGol
gi:

-c
oatedv
esi
cl
es-ar
eves
icl
eswhos
ememb
ranehasoni
tss
urf
acea
l
ayerofp
rot
einc
oat

-COP’s-non-c
lat
hri
n-c
oat
edv
esi
cl
es(
par
tofnond
isc
rimi
nat
ory
pathway)

-r
equi
resGTPasener
gys
our
ce

-Ret
aini
ngp
rot
einsi
nER-p
rot
einsc
ont
ain(
Lys
,As
p-Gl
u-Leu)

-e.
g.d
isul
fi
dei
somer
ase

-mol
ecul
archap
erones-i
nvol
vedi
npr
otei
nfol
dingandr
emai
nins
ide
comp
artment
 -Targetingvesi
clesduri
ngt ransp
ortoccursbyspeci
fic
int
erac ti
onsbetweenproteinslocat
edonmemb ranesof
vesi
cles(V-SNAREp r
oteins)andr ec
ept
or sontarget
memb rane(t-SNAREp r
oteins)

-e.
g.V-SNAREfromERbind
stot-
SNAREcisGol
ginott
-SNAREinl
ysos
ome)

5)TransGolgiNetwork(TGN)-anet workofinterc
onnectedtubular
el
ementsatt hetransendoft heGol
gicompl
ext hatsort
sandt argets
prot
einsfordeli
verytotheirult
imat
ec el
lul
ar/extrac
ell
ulard
es t
ination

-2t
ypesofv
esi
cl
es:

1)
nons
elec
tiv
enon-c
lat
hri
n

2)
sel
ect
ive,c
lat
hri
n-c
oat
edv
esi
cl
es

-Exocytosi
s-p r
oces sofmemb ranefusi
onandcontentd i
scharged uri
ngwhichthe
memb r
aneofas ec
r etorygranulecomei
ntocontactwiththeov erlyi
ngp l
asmamembrane
withwhichitfuses,therebyforminganopeni
ngt hroughwhicht hecontentsofthe
granul
ec anbereleas ed

I
V.As
ymmet
ryofMemb
rane:

-memb
ranesar
isef
romp
re-exi
sti
ngmemb
ranes

-as
ymmet r
icmembranes-est
abli
shedi
nER-memb
ranep
ass
esb
ypr
oces
sof
bud
ding/
fusion Gol
gi ves
icl
es

-Int
egralmembraneprot
einscont
ainhy
drop
hob
icami
noac
ids
,whi
chanc
horp
rot
eini
n
membrane(st
op-trans
fersequences
)

-Sy
nthes
isofmemb
ranel
ipi
ds-s
ynt
hes
izedi
nER

-exc
ept
ions
:sp
hingomy
eli
nandgl
ycol
ipi
ds-s
tar
tinER,f
ini
shesi
ntheGol
gi

1.Phos
phol
ipi
ds:

-enzy
mesar
eloc
atedonERasi
ntegr
alp
rot
eins
;ac
tiv
esi
tef
acesc
ytos
ol

-i
nser
tedi
nto½ofb
ilay
erf
aci
ngc
ytos
ol

-mov
etoop
pos
ite½ofb
ilay
erund
erd
irec
tionoff
li
ppas
es

-phosphol
ipi
dexc
hangep
rot
eins-t
rans
por
tphos
phol
ipi
dsf
romonec
omp
art
mentt
oanot
her
compar
t ment

V.Cel
lul
arup
take:
1)p
hagoc
ytos
is-engul
fmentofp
art
icul
atemat
eri
al

2)end
ocy
t osi
s-proc
essb
ywhichprot
einsatt
hes
urf
aceoft
hec
ell
arei
nter
nal
ized
,bei
ngt
rans
por
ted
int
othecellwi
thi
nmembr
anousves
icl
es

a)b
ulk-p
has
e-unr
egul
atedend
ocy
tos
is

b
)rec
ept
or-med
iat
ed(
RMF)-s
pec
ifi
cend
ocy
tos
is