;D

÷
 Chapterceireoombination
Recombination sorting
•

of alleles into new combinations

[P generation] A ABB X aabb

CAB [ Gametes] ④
Fertilization
.-

t
[F , generation] AdB@ Gamete
more purple,
✓ Formation
# long flowers
than I

ABO ④ ①ba⑨ expected

NON RECOMBINANT RECOMBINANT

Norrlhdependentttssortment
Not all genes
independently
•
assort

•
1905 Bateson Saunders & Punnett -7 Flower color
, ,
/ Pollen shape
↳
parental generation phenotypes occurred more
frequently than expected in Fz
generation

Linkedgenesi
•
the same
genes located close together on chromosome

↳ Travel together in meiosis & do not assort

independently → arrive @ same destination together
↳ Crossing over causes recombination bln them

Crossing
•

>
Linked genes segregate together ,
while
crossing over produces recombination bln them
>
Crossing over results in recombination ; breaks up
( keeps genes together) ( mixes up → new gene
association of genes that are close together on the same chromosome
d f combos )
>
Linkage & crossing over
=
OPPOSITES
happened)
* When random assortment occurs (a cross over
-

> A
single crossover produces
¥ recombinant & tz non recombinant
Observed
freauenoy of recombination =
5090
gametes gametes

↳Nbinantg¥aentagamee) :
gametes that contain
only original combinations of alleles that were present in the parent

MD IMD MD Imd
-

X mdlmd →

MD Imd
-

X mdlmd → MD or Md

NO new combos of the

2 traits appear in the
offspring b/c the genes affecting the 2 traits are
completely linked & inherited
together → no independent assortment occurs

↳
Recombinantgametes w/ new combinations of alleles

MD Imd → MD Md
-

or md or or MD

Independent
-

assortment occurs

Progeny
-

w/ new combos of traits formed from recombinant gametes

→ Recombinant Progeny
 # of recombinant progeny
100%
Recombination ( %
×
totality
-

:
Of recombinant
progeny produced in a cross )
↳ Allows us to predict the proportions of offspring expected for a cross entailing linked
genes
↳
> CWSsing over & is responsible
for Genes < 50%
occurs
during meiosis recombination are linked when re combo .

frequency
↳ Genes may its Meiosis 1
chromosome to in
switch
from a
homolog by crossing over

↳
In Meiosis 2 , genes that linked will then assort I end different gametes
are
normally independently Up in

>
The closer the 2 genes less will occur bln the
are to each other the
frequently a cross over
genes
-

>
Coupling ( Cis) & Repulsion (trans) configurations are revealed via Test cross

Hhoonmoisoagme ① "'
to -

Barbara McClintock & Harriet Creighton provided evidence that genes are located on chromosomes

knob 9
-

on chromosome in corn
-

Special b/c when crossing heterozygote for kernel color & l

starchy waxy traits in
to Wxwx plant result had abnormal
repulsion cc
, distinguishable ends on Ch 9
,

[ Ccwxwx x ccwxwx ]

McClintock & Creighton predicted physical structure of chromosomes

-

of plants that were

doubly homozygous recessive, confirming the chromosome theory of heredity

µ mob

cwx-xcWX-GEqfsodET.tw#ILhB
A
Extra piece

Wx
c c w x x

K¥908

Howcanwet lifgenesarelinkedorhot.ae
•
¥
A
each should be result it independently

Chi square test can be used to determine if 2 genes

assorted ( not linked)

assorting independently
-

are
Genelllappingtchwmosomeso
Genes far
away from each other , or
genes on separate chromosomes segregate independently
•
Genes that linked WI distance
frequency roughly dependent
are other
segregate a upon their from each

Recombination frequencies used to determine relative gene location on chromosomes

* A two Strand double

-

crossover bln 2 linked genes produces only gametes

I
non recombinant

↳ Double 2 distant genes

crossovers bln the same chromosome
may occur
frequently on

* Three types of crossovers can take place among

3 linked loci

txonlyhave
gene
altered
middle
/
* Double crossovers occur less
frequently
due to the inhibition of it from
the crossover of a
single gene that

stops it

•
We can map linked genes based on their frequencies
↳ Can in the middle based ( double crossover) event
find the
gene on the least
frequent

in this 3-point test cross , the

-

helps to put the the correct order

genes in
-

( St)
recessive mutations scarlet
eyes ,
after finding middle gene , &
indicating the

color ( e) , & spineless bristles crossovers

ebony body on the map
( SS ) are @ 3 linked loci

YOU can know there will be 8 different the relative distance of the outer 2 genes to
- -

F , gen the 3 Non recombinant the middle one can be calculated using the
progeny due
to
genes

} frequently
.

being put to
power of 2 ( 32=8) produced most multiplication rule

( scarlet, Ebony ,

spineless)

can deduce that the double

-

crossover
the least This is
occurs
frequently .

the spineless gene → must be in middle of

other 2
genes

37:iobmebicnassoi
"

produced least * Distances bln genes within

frequently
a
linkage group are in map units
physicalmappinMapping
gforlocatingGenesonchwmosomyl.DE
let on → determines
chromosomal location of a
gene
↳
An individual Caa)
homozygous for a recessive mutation in the gene of interest is crossed WI an individual heterozygous for a deletion

If gene
-

of interest is in the deletion then

region ,

half of
progeny
will
display MUTANT
phenotype

If gene of interest is NOI in deletion then

region ,

ALL progeny will be wild type

2 .
Somatic -

cell hybridization →
determines which chromosome contains
gene of interest

↳
Hybridizing 2 cells of different species . Fuse together & form a hetero
Kanyon

/ produces different cell lines w/ different combos of genetic info

\
can look for gene of interest by looking for protein product

* CONCLUSION If the cell line wt but

:
gene product is present in a an intact chromosome
missing
from line WI chromosome deletion the product must be
gene for that
a a located in
,
the deleted region

3 In situ hybridization →
determines chromosomal location
.
of a
gene
↳ Uses labeled DNA , RNA , modified nucleic acids to specific DNA tRNA sequence in
a
complementary or strand localize a a

portion of tissue

↳ Different chromosomes have specific fluoresce specific ( different) colors

probes that
 BauerialdviralGeneticssy.sk#
Bacteria & Viruses
•
can be good model systems for studying genetics

÷÷÷÷÷:÷÷÷÷÷.in?.: :.: : : : : :amnicaijconmnnmi: ne

gene structure organization
-

gene regulation
-

in bacteria

. .

Advantages G.e.n.e.ti.c.S.N.d.i.es E

¥
.
.
.in
.
.

>
Many small
> •
size &
rapid reproduction progeny produced genome
>
Haploid genome dominant recessive) rapid reproduction
②
all mutations expressed (
directly
-

no
-

sa: in:O:c::÷:÷:÷"
" """

s's:c:c:
"

; mins :L: :::::: engineering memo.

>
Techniques available
for isolating 1 manipulating genes
7 Medical importance
•
best studied DNA on
planet
>
Can be to produce substances of commercial
genetically engineered Value

Individual
•

cells reproduce to form colonies This .

growth allows the isolation of clones of bacterial cells , separate from cells in
Other colonies -8 solid medium
grown on

Mutant bacterial
•

strains can be isolated via nutritional requirements via REPLICA PLATING

↳ Bacteria
may mutate to gain the
ability to
grow on certain selective media

BacterialGeneticsysle.ms specific DNA where DNA replication is

; iaueence
Single circular
•
chromosomes
,
/ necessary for DNA &

1 origin
Rlplpifainey Ceri )
•
have of replication
to grow
genomes plasmids
→

↳ DNA polymerase has to be shown where to start

making new nucleotides

↳ p
Must have a primer ( usually RNA primer) to show DNA polymerase
↳ Also how plasmids replicate
NOT in all bacterial

Plasmids -8 Circular its a

genomes
piece of DNA outside of chromosome that replicates
•
on own ,

↳ chromosome, but have several different kinds of plasmids

Only one can

↳ encode ( ex like resistance)

variety of info .

genetic advantages antibiotic

K
Pteplication similar to bacterial chromosome ( 1 origin of replication)

Ef
s
±

Bacterial Replication @ Ori -

Ori :
this DNA can be transferred of
Grene ignorance?,%£"ploiysmeiaesendbsitnaanstomovingnidn
'

plasmid
instead of the primer
-

g
is
§
F
-

-
 Plasmids replicate
•

independently ,
but in a
fashion similar to that of the bacterial chromosome

↳
Replication begins @ origin of replication Cori V ) & continues around circle .
Can take place in one direction or both

* Insertion sequences ( IS 3 & IS 2)

control insertion into bacterial

chromosome & excision from it

Gansfer ( horizontal -
-
adult cell → adult cell ; vertical =
parent → offspring)

1 Transformation
"
"
.
:
uptake of naked DNA directly from environment
Bacterial dies &
ex cell
lyses DNA into environment & other cells take it up via transformation
-

open
-
.

only competent cells are capable of DNA * Joshua

I-BEertfafo.de?fYiosnfaho+we-dthatLederberg'sexcnangereo
-

uptake
-

Edward Tatum demonstrated

Lederberg & genetic
exchange in 1946 .

2. Transduction
phage
:
mediated transfer of DNA
-

↳Generalizedtransdvction Lytic
oh
E
( breaks bacteria cell open → releases
phages)
.

phage infects bacterial host cell

§
'

•
bacterial chromosome is broken into pieces
genes become incorporated few
e-
or
.
some of the bacterial into a
phages
E cell lysis ( piece of bacterial chromosome in coat)
diving phages phage
"
releases trans

is s
N
.
if the phage transfers bacterial
genes to another bacterium, recombination
may take place I produce a transducer bacterial
o

J E cell
in B from bacterial
s f
•
Any gene can be transferred one

Es
g
cell to another by a virus

¥f
§
•
Viral DNA left out by mistake & bacterial DNA packaged instead

u n

E I
O

-
f
o
e
u ↳ Specialized
-
transduction : Lysogenic ( phage DNA integrated into bacterial DNA -8 pro phage)
•

transfer & a small 90 of bacterial DNA wt the viral

packaging of
genome
•

remains inactive , replicated w/ new bacterium , later enters lytic cycle

Requires lysogenic bacteriophages

•

( specific genes ONLY )

•
Genes near special sites on bacterial chromosome are transferred
from one bacterium to another

•
There are attachment sites on both the bacterial chromosome
/
& viral DNA

Unstable trans duct ants when bacterial chromosome

takes up a 2nd viral DNA while it
already has

oney
3. Conjugation :
transfer via cell -
to cell
- contact ; pilus -

mediated
the 2 Plasmid passes from recipient
pore opens ,
connecting cytoplasm donor to
•
.

.
Donor cell has Ffactor → contains
genes that
regulate transfer into bacterial cell , replication & ,
insertion into bacterial chromosome
+
K
↳ plasmid that enables transfer of F factor whole
genetic material from donor to recipient cell F
fertility plasmid
-
=

I
-

g
. .

£ 7
Cells WI F factor Ft ( present in the cell ) DONOR
In circular plasmid
=
as separate

§ .
-
>
* Epis0M plasmid capable of chromosome
-
-
E t
Cells without F factor = F -

RECIPIENT integration
E
& o

>
of Ert F factor is an epi some (plasmid that can
integrate into bacterial chromosomes that requires an Origin of Replication &
t '
( pili)
genes necessary for
conjugation
t

↳ I

>
s s If the entire F factor is transferred into the recipient F -

cell , that cell becomes Ft

O O
f
cell first 15 ' end =
Un nicked Strand)
- '
7 The 5 end acts as head of the arrow & enters recipient
•
Sex-pi connects cells during conjugation ; donor makes pilus & extends it to the recipient

•
Cells must be physically close to one another for conjugation to occur

The F factor is transferred during conjugation bln Ft and F cell → BUI F factor didn't responsible
contain for all the traits
-

an genes
for growth of Lederberg 's mutants

↳ mate
an Ft WI an F- , recipient F
-

turns into Ft (2 Ft cells =

result)

( integrated)
•Hfrce bacterial cell who has had an F factor present ,
integrated into its chromosome .
F factor -5 Bacterial chromosome

↳
Crossover can occur bln the bacterial chromosome & the F factor to form a high freq .
of replication Utfr) cell
↳ The orientation of the F factor Hfr cell determines direction of
in an
gene transfer
↳
Genes closest to arrow head transfer to recipient first & then moves down
strain

↳ Formation of
an Strain : Hfr
# = insertion
sequence

Homologous insertion sequences align ,

a crossover occurs R recombination
-
,

takes place
The Or IT can insert itself wherever
,

# doesn't have to

regions
be bln pro d Iac

↳ Bacterial Hfr cell to an F

genes may be transferred from an cell in
conjugation
-

* This process is often

interrupted , so the recipient
stays F ble it didn't
-

get the on the

genes
tra region
<
However , recipient
did gain some
bacterial DNA
 •
F'ce# cells containing an F plasmid present as a separate circular plasmid carrying some bacterial
genes
↳ An Hfr cell be converted into F
'
cell when the F factor excises from the bacterial
may an

chromosome & carries bacterial genes with it .

Conjugation produces a partial diploid .

↳ The F factor OUT just like it did IN It takes bacterial DNA

can recombine . some of the adjacent
from the host when this occurs .

↳F' is the F plasmid carrying bacterial genes

CharacteristicsofE.colialls#

roleinconjvgation-Resultsofcµo÷n¥juIYgma¥t±io¥nfbE.¥t÷n/t
differenttypesofFfact# -

TIE FF-aciorcharacen.si

'

÷::
Present " "" ""

:;;: "
.

Present, integrated into

Hft bacterial chromosome High frequency
-
donor Hft X F -

7- Hfr I
,
F- ( no change)

present as separate circular

f-
,
F,XF 2 F cells ( F FF )
'
-

' -

DNA , Donor
carrying some bacterial genes
t

*
Rarely F cell becomes Ft in Hfr X F if
- -

entire chromosome transferred during

conjugation

IntemptedconjvgationtomapBacterial.GE#
•

Jacob & Wollman used interrupted conjugation to map bacterial

-

genes
Interrupt conjugation different times → different amount of time
-

@ amounts of genes passed depending on

The transfer time indicates the order & relative distances bln →
can be used to construct
genes genetic map

Rplasmids conjugative plasmids

•

that carry antibiotic resistance genes

↳ it is cells, this is what makes antibiotic resistance hard combat
possible to have trans species conjugation in bacterial to
-
Transformationcanbevsedtomapbacterial.ge#
is
•
The rate of cotransformation to the
inversely proportional distances bln genes
•
In order
for this to work , both strands must be competent

More transformation → more → more evolution

•

genetic information

The larger it takes

genes the
•
the distance bln the more time

Bacteriophages:ViwsesthatinfectRreplicatewithinbacten
•
Offer a mechanism for the transfer of DNA bln bacterial cells
•
Plaque Clear patches of lyse d cells on a lawn of bacteria

↳ lytic cycle ( generalized

phages use transduction) to cause plaques

Lederberg & Zinder phages transferred DNA bln bacteria

•

showed that not all direct contact →

genetic exchange requires
Some bacteriophages have 2 alternative life
•

cycles : lytic &

lysogenic
t.LI/tiCnCycleni- the NORMAL process of viral reproduction ,
involving penetration of the cell membrane , nucleic acid synthesis ,
&
lysis of the host cell
>
Phage infects cell ,
having viral DNA
circularizing &
remaining separate for host DNA

>
Phage then replicates ,
& bacterial cells are opened Uysed) to release
newly replicated phages
> T4 phage ( infects E coli in stomachs) only capable lytic cycle
.

of

>
During lytic cycle , enzymes for lysing membrane of host cell produced ; genes for proteins in the capsid encoded

2.
Lysogeniccyclei phage DNA is incorporated into the host
genome & passed on to subsequent generations
>
Virus lays dormant until host conditioner deteriorate (stress low nutrients) , then viral DNA excises itself from
,

genome of the
former host & ent the lytic
cycle
>
important for specialized transduction
> all have viral DNA in their bacterial DNA
* Creates pro phage
→
bacterial
progeny in it
long host cells genome w/
phage DNA injected
> More advantageous for viral DNA as as
healthy
 -
l I l I IlI I
l l l
f. . .
.
.
r r r

-
Chapter
. -
8 : chromosome Variation
t '
l
I / / / I l
l '
' ' '
l
' '
l ' '
l l
y
•
ChWMOS0MeMVtatiOh# Variations in the number / structure of chromosomes

T.me?a.mno.m:someMmomoaam-
mum
centromere in middle ; both arms
equal lengths
F.iqfe.IT/
¥¥¥f•¥¥¥
2.SUbmetacehtric.im centromere displaced toward one end → One
long arm & one short arm

3. Acrocehtricin Centromere is near one end and

, producing a
long arm a knob at the other end

4. Twenty centromere is at or near the end chromosome

very of the

•
Karyotype the complete set of chromosomes possessed by an
organism
→ picture of set of chromosomes
↳ Giemsa G bands in DNA which
dye reveals distinguish of DNA that are rich in
-

, areas

adenine thymine LA T) base pairs

-
-

Bar in fruit flies results from

phenotype
°

an X -
linked duplication
Lp unequal crossing over produces Bar
Typesofchromosome.MU/-ati# and double Bar mutations
-

•
.
BE .AM?l.h..g.C.h.h..e.h..tS..
.
:
alter of chromosomes
↳
Duplications :
part of the chromosome is doubled

↳
Looping out of the duplicated
and deletions
region during prophase 1 is characteristic of
heterozygotes
-

↳
Effects of duplications include unbalanced
gene dosage
→
developmental abnormalities

↳
Deletions : the loss of a chromosome segment
↳ Deletions prophase I in
also lead to looping out of chromosomes in
heterozygotes
↳ Pseudo dominance can occur when recessive alleles are expressed due to the deletion of a

dominant allele
Both pseudodominance & haplo deletions
insufficiency are consequences of heterozygous
↳ Genes haplo insufficient when
are the
single copy results in
gene dosage too low to
a

in
Affect ( ex .
notch gene fruit flies

↳ Inversions
a chromosome segment is inverted turned 180)
↳ May be (all on one arm) centric ( centromere switched around , too)
pgra
centric or
pgri
Para -
-
next to ; does Not include centromere peri = around ; includes centromere

Effectsoflnvers.io#
•

when inversions interrupt individual genes, their expression is destroyed

-

genes moved expressed differently due to positional effects

-

to different locations can be

-

heterozygous inversions lead to decreased

crossing over in the inverted region
when it lead to
\
crossing over occurs , can non viable
gametes
-
-
 ↳
Translocationsmovement of genetic material bln nonhomologous chromosomes OR within same chromosome

↳
May be reciprocal ( mutual switching of DNA) or nonreciprocal ( all DNA from donor moved to recipient & none
given to donor)

↳Effect .
like inversions translocations can interrupt individual genes , destroying their expression
,

• also like inversions , positional effects such as altered linkage & expression can result from moving genes to
new locations
translocated region can also lead to non viable gametes
crossing over in the
-
•

€fV Robertsonian Translocation → Short arm of one aero centric chromosome is exchanged w/ the long arm of
another RESULTS reduction
=
I t 1
. in in chromosome number met acentric chromosome
fragment
↳G
banding reveals that a Robertson ian translocation in a human ancestor switched the long
-

& short arms of the 2 acrocentric chromosomes that are still found in 3 other primates
today .

This translocation created the large meta centric human chromosome 2 .

In
•

individual reciprocal translocation , cross like structures homologous pairing

an
heterozygous for a form in

Fragilesitesi chromosomal regions

•

susceptible to breakage under certain conditions

> >
Break easily → loss of info
genetic Fragile X syndrome in humans causes retardation & is due to an increase in tri nucleotide repeats

Aneuploidy
•
number of individual chromosomes is altered 1 affects just one chromosome ; normally an increase I decrease of 112 chromosomes

↳ CAVSesi.me is lost
chromosomes can be lost during mitosis I meiosis if centromere
-

* results in somatic
cell differences
Lex produced in Robertson ian translocation)
may fail
small chromosomes to those
-

segregate .

q ( non gametes)
-

nondisjunction of replicated pairs of sister chromatids during mitosis can result in cells w/ extra or
missing chromosomes

↳ the
gametes that result from meiosis WI nondisjunction combine WI a
gamete that results from normal meiosis
to
produce aneuploid Zygotes

↳ Types :
I Null i so
(2n-2)2
loss of BOTH chromosomes of Individuals
°

my a pair are
.
Mr -
.

-
.

MONO SO loss of ONE chromosome of ( 2h t)

my
°

pair Individuals are

-

a
.

.
#
#
#

3. Trisomy : C2ntD
gaineexrachwmosom.ttindividuals are

l2ht2)↳IhhUMans:m
4.TN#:gairahomoogouschwmosomes .
Individuals are

Sex-linked -0 Turner syndrome ( one X chromosome) & Klinefelter syndrome (xxy ) q Mostaarietosoimnaleaneuploids
•

•
AUDIT Down syndrome (trisomy 21) , Edward syndrome (trisomy 18) , Patau syndrome (trisomy 13)
Polyploidy
•
one or more complete sets
of chromosomes are added

↳Cctvsesn :
nondisjunction in mitosis or meiosis

↳ types AyplOidyT Condition

•
in which all sets of chromosomes of derived
single species
a
polyploid individual are from a

↳ can arise
through nondisjunction in mitosis or meiosis

Atlopolypidy→
•

condition in which the sets of chromosomes of a polyploid individual are derived from 2 or more species ( sterile)

↳
Agricultural examples :
potato , banana, peanut, etc .
 ChapterlO:DNAstNcto#
keycharacteristicsofceneticmoleculesoo
-

large
genetic material encodes amounts of complex information required for life
•

genetic information must be

accurately replicated and
segregated into
progeny cells
•
the genetic material is responsible for the
phenotype
•
nature of different proteins gives the properties to the cell

Historyofovrvnderstandingoftdhlttandcenlsl
.

first described (
Nucleus) 1833

2. Cell theory proposed ( 1839)

3 .
Mendel 's work
first published ( 1866 )
4 DNA first discovered in nuclei of white blood cells ( 1869)
.

5 Histones isolated from nucleus 11884)

.

6. Recognition that )
nucleus is the physical basis of heredity ( 1887
7. DNA contains nitrogenous bases ( late 1800 's)
8 Mendel 's work rediscovered ( 1900)
.

9. Tetranucleotide A G GT ( faked
Theory proposed 11910) → DNA made of equal parts of , ,

10 .

Transforming principle first demonstrated ( 1928) → Bacteria capable of transferring genetic into via transformation

l l .

Avery MacLeod
, ,
&
McCarty demonstrate that the
transforming principle IS DNA ( 1944)
12 X
ray diffraction studier of DNA 11947)
-

13 Char
graff discovers regularity in base ratios of DNA ( 1948)
.

14
Hershey Chase Experiment → DNA is genetic material using bacteriophages 11952)
.
-

% finger
Watson & Crick devise helical structure of DNA ( 1953)
, shows that rome viruses use RNA as genetic material ( 1956)

•
Phoebus Aaron Levene discovered that DNA was a polymer of nucleotides

phosphate
r =
Nucleotide

Lead to Tetranucleotide
Theory
-

By 1890 ,
chromatin in the nucleus was accepted as the genetic storeroom .
BUT . . . was DNA or protein responsible for heredity?
↳ Both to be
types of macromolecules known present in the nucleus
Obviously
were
* this was
wrong
↳ Proteins were more complex and therefore likely to encode the complexity of life 's molecules

that DNA
Up The tetra nucleotide
theory implied simple to the vast amount of information associated with the
was too encode

Phenotypes of cells

In 1928 Fred Griffith demonstrated transformation in

-

, bacteria but could not

, explain the mechanism

↳ In situation Cd ) the nonvirulent cells

by the virulent cells DNA , causing it to
'
,
were taken up

kill the mouse .

Autopsy revealed both virulent & nonvirulent bacteria in the dead mouse

* Avery MacLeod
, ,
& McCarty discovered that the
"

transforming principle
"

was DNA

\
-

Fein:¥÷¥¥h÷:*:#stain
.
=
RNA =/ genetic info

• protease (destroys proteins) did

NOT break down
genetic info
in virulent strain
=
proteins # genetic info

•
DNase (destroys DNA) DID
break down info in
genetic
virulent strain
= DNA is genetic into ✓

William
-

Ashbury began using X-ray diffraction to

study DNA in
1947 .

* Erwin chargaff disproved

Tetra nucleotide
Theory in 1948
( ratios of A =
T and G- G )
t#ChaExp#
-

•
T2 bacteriophage infects E . Coli -7 the
phage contained DNase to break down host DNA
↳ protein coats of phages were not found in results → did not hold
genetic into → it was what was

inside of protein coats -

DNA that was transmitted
-

& Chase demonstrated that DNA is the genetic

Hershey hot bacteriophages
• -

protein
-

material in

Protein coats
remained

r 7
DNA
transmitted

X ray diffraction data gathered by Rosalind Franklin

•

in Maurice Wilkins laboratory by James Watson & Francis Crick

-
'
was used
to model the 3 dimensional helical of DNA in 1953
-

structure

In 1956 , Heinz Fraenkel -

Con rat and singer demonstrated that RNA ( hot DNA) is the genetic material of viruses using the Tobacco Mosaic Vins (T MV)
 DNA consists of two complementary and antiparallel nucleotide strands that
•

* The double helical structure

formadwble.net
provides mechanism for heredity → -

complementation of antiparallel °
strands provides templates for
exact replication and
7
-
I Structure : string of nucleotides joined by phosphodiester linkages
transcription
> 8¥: three dimensional structure originally modeled , by Watson & Crick
↳ Both

mzgfh g f¥¥÷÷i÷÷
DNA & RNA can form special secondary structures -0 Hairpins
:
:* Fine :&::÷i÷÷÷:÷::%÷::÷:÷n.sn#:::r::ioni.n:.en:*mmiax:ments
:÷in as .

•
When the
-

phosphodiester linkage connects complementary sequences are

formed
'
contiguous stem is
'
5 phosphate group and 3 OH a

[
-
-
,

with loop
group of adjoining nucleotides inverted
no

complements

>3°StrVCtvre:higher -

order folding that allows DNA to be packed into confined space of cell
<
Psvpercoilingi DNA helix subjected to strain by being over wound or Unwound

↳ controlled by topoisomerase enzymes

↳ Most DNA is (unwound) which eases the separation
cellular
negatively super coiled ,

of nucleotide strands during replication & transcription and allows the DNA
to be packed into small spaces

↳ results in more condensed chromosome forms

BvildingBlockmodelofDNAS.net
* Ribose (RNA) has
phosphate binds to
sugar hydroxyl group

y
OH )
'
@ 2 carbon
'
@ 5 carbon ( -

Base bound
'
* Deoxyribose ( DNA) has an H

f
' carbon

f
@ '
2 carbon
sugar
-

phosphate
backbone
sugar has
5 carbons
Nucleotide =

Monomer of DNA -

DNANvaeotid
Purines Adenine Guanine ( bigger
>

,
bases → have 2
rings) > pairanother
w/ one
>
Pyrimidines Cytosine Thymine , ,
Uracil ( 7-
ring)
DNAcanassumeseveralaetemativesecondarystnctvreso.vn
der normal
physiological conditions,

DNA is typically in Biform ( classic right hand double helix)

-

Afan : thicker right

-

handed duplex w/ shorter distances bln base pairs ( RNA -

DNA & RNA RNA)
-

L
from complexing WI proteins ; more UV resistant than other forms

•
Zformi left handed helical
-

duplex ; longer A thinner

RIVAL contains ribose

sugar . Adenine pairs w/ Uracil ; Phosphodiester bonds like DNA

↳ also form hairpin structures

can
secondary

o.CM/-ralDOgmaOfM0leCUlarBiOl0g# pathways of information transfer within the cell

Wmtw A DNA → DNA

replication ( DNA polymerase)

Transcription DONA
( RNA polymerase)

w/¥
n
V
DNA → RNA Reverse
transcription

Nw¥¥n

protein
RNA

Translation replication

•!i•:•m•!•P
'

••

transcribed> 'tI
DNA RNA >
protein * RNA can be replicated & undergo reverse
① Replication
transcription to form DNA
( primarily in certain classes of viruses)
 Bacterial DNA
highly folded
•
is into a series twisted loops
of

* DNA organization in
eukaryotes is

necessary and dependent upon formation

Of 30 structures

Chromosome Structure
•
Eukaryotic positive proteins that keep

(E)
> Linear double stranded
I
, neg charged
. DNA tightly wound together
⇐ 7 Nucleosomes ( DNA wound around histones)
7 Chromatin ( multiple folded nucleosomes )

Chromosome ( protein t of DNA)

E
¥
7
single molecule

Genome ( sum
E

organism's DNA)
-
E > total of an

Histones proteins that help organize eukaryotic chromosomes

•

↳ each nucleosome is made up of histone proteins UPDNA negative charge ; winds =

around positive histories
↳ 9 total ; 8 of them make up the core around which DNA coils
↳ Chromatin is not
tightly bound together

Nucleosomes form chromatin fibers

•

stack to

130
nm chromatin

\ De condensed to

Types
m
Chromatin
ofu m
reveal nucleosomes

Euchromatin
•
less condensed , found on chromosome arms
,
contains unique DNA sequences , contains most
genes ,
crossovers common

Heterochromatin more condensed , found @ centromeres , telomeres other specific places, made of repeated sequences , contains few
•
,

genes crossovers uncommon

,
 Chapter l l : chromosome Structure & Transposable Elements

In complex structure WI several

eukaryotes chromatin has highly layers of organization
•

,
a

↳ nucleosome made Of histone Octa Mer →

complex of 8 histone proteins found @ center of a nucleosome core particle
-

Oct amer contains 2 copies each of four different proteins : H 2A , H2 B, H 3, H 4

•
Histone acts in a clamp -
like
fashion to help stabilize

DNA about the nucleosome

•Histonetailsaresubjecttomodification&helpregulategeneexp

=
-

Acetylation modifies the lysine amino acid

side chains on histone tails to make
DNA more accessible → neutralizes
= positive charge in histone tails & removes
the strong interaction bln It ) histone protein
-

& t) DNA

•
Chromosomal puffs →
regions of relaxed chromatin where active transcription is
taking place
# more accessible to transcription of DNA)
 Stncturalcomponentsoftukaryoticchwmosomest
•

Centromeres
-

constricted region to which the spindle fibers attach during mitosis & meiosis
-

contain centromere sequences that affect function ( particular sequences repeated many times )
<
don't encode proteins → specific centromere proteins bind to centromere sequences & sites for spindle fibers to attach
they provide anchor

Importance If chromosome is broken , some DNA be lost

may
-
:

Consist of heterochromatin lightly wound

so stay
-

> telomeres
ends stay together
sequences @ the ends of chromosome that helps chromosome
-

-
contain specific telomere sequences that are repeated and are the site of protein interactions telomere
cut short
by 3 nucleotides replication during
,
-

help w/ DNA replication @ ends of chromosomes

-

DNA @ ends of eukaryotic chromosomes consist of telomere sequences -

centromere

#t -

loop helps protect ends of DNA

'
telomere
<
noncoding region (no genes here)
so remain heterochromatin for
most of replication

Artificialchromosomes
•

•
Artificial chromosomes for yeast (YA Cs) ,
bacteria ( BAG) ,
& mammals ( MAG) have been synthesized by researchers & can harbor
genetic information just as native chromosomes do

In
eukaryotes 3 elements are required to make an artificial chromosome :
•

Te loment sequences specific for the organism * Genome necessarily directly related to
-

size not
Centromere sequences specific
for the organism complexity of the organism
-

. . .

one or more Origins of Replication corn & salamanders have larger genome
than humans do
TransposableEIementstumpin.Ge.no/Transposo#
•
transposons DNA sequences that can move about in the
genome
↳
DNA-onty.me :
DNA fragments transpose directly from DNA segment to DNA segment producing
,
a DNA copy that either does . . .

>
Replicativetranspositiori ( aka copy & paste) A new copy of the transposon is introduced @ a new site , while the
.

old copy of the transposon remains behind at the

original site
Requires single strand breaks replication I resolution
-

, ,
.
# Of transposons increases) (
paste) The transposon is excised from the old
>
NOnreplicalivetranspositioni.laka cut & .
site & inserted @ a new
site without any increase in the number of its copies

↳Rethtransposons.me RNA intermediate RNA is transcribed from the DNA transposon d is then
transpose through an .

copied back DNA

into
by reverse transcriptase Replicative transposition only Common in eukaryotes
.
.

• Often a cause of mutations

Universally among forms of life ( ubiquitous )
present Yellow
-
-
•

✓ transposon
Duplications occur bln 2
Comprise high percentage of genome 64570 in humans )
•

/ transposons

Transposition movement of transposons into genes; can alter gene function ; often generate chromosomal rearrangements
•

↳
TranspoSase enzyme ( catalyzes transposition) makes staggered cuts in the target DNA leaving short single stranded , ,
-

pieces of DNA on either side of the transposon

↳A transposon inserts itself into the DNA and flanking direct repeats are formed

Roles of transposons in Genome Evolution

-
-

. . . . .

transposons introduced genome can colonize it & spread throughout cover time not immediately)
• " "
into a ,

functions
•
movement of transposons into genes or their
regulatory sequences can drastically alter their
•
multiple copies of transposons provide sequences that can act as targets of homologous recombination
Mechanisation ( copy
•
& paste) * Required
=
for replicative transposition
*
Replication
K

* single strand
-

*Resolution
breaks

•
The transposable element (transposon) is & contains several genes, of which is transposal
flanked by inverted repeat sequences @ each end one .

• In the target plasmid , Transpo Sase acts @

region of insertion & the target plasmid by transposal leaving staggered ends ( b)
is cleaved ,

plasmid containing of it These ends join w/ the cut ends of the target plasmid ( c, d)
•
Transpo sase also cleaves the the transposon @ the ends .

•
The single
-
stranded regions of the DNA are replicated (e) → resulting genome co integrate ; contains original transposon t new copy of it
=

•
Recombination occurs & original donor plasmid t target plasmid w/ new copy of transposon are
resulting products ( )
g

RetNtransposonstransposethwughRNAintermediat
-

<
Exclusive to
Retrotransposons comprise 45% of our genomes .

Eukaryotes
L
Red & white color in grapes resulted from insertion ( white) & deletion ( red) of a retro transposon

I Retro transposon is transcribed into RNA

by RNA polymerase
.

Upi transposon needs to be inserted into new region of DNA but it

problem
m
: retro ,

it is in RNA . Needs to be in DNA instead

2 RNA . is reverse transcribed into double stranded DNA

-

using reverse transcriptase

3. target genome, making staggered

Integrase cuts breaks

4. Retrotransposon pasted into target gene ; remaining gaps are filled

by replicating
the DNA DNA
on opposite sides
using polymerase

5. DNA
ligase glues the segments together

Insertion sequences LIS)

-

are simple transposable elements found in bacteria → transposase

commonly associated WI this

* only carries genes

I
required for its
movement

composite transposons in bacteria include 2 IS elements & the DNA bln them (Tn =
Composite transposon)

* Can carry other such the antibiotic

genes as

resistance Het) gene

-

Some bY replicate via a transposition type event

- -8 Md is a
transposing bacteriophage
↳ other examples :
variegated ( different colored) kernels in corn ;
-

Ty transposon in yeast

Characteristicsof2majordassesoftransposabkgeneticeleme

④I HASSID
* Retro transposons * DNA only -

:/
-

Long terminal direct repeats ; Short terminal inverted repeats ;

StNdW short flanking direct repeats @
Short flanking direct repeats
target site @ target site

Etta "
i:S: 're:insanities: "
"

sina.smaseg.es,
Transposition :

By RNA intermediate
-

Through DNA
(replicative or non replicative)

Examplesi Ty (yeast) , copia (Drosophila) , ISI CE . coli ) ,

Tn 3 ( E Coli ),
.

-
Alu ( human) Ac Ds ( maize)
, ,

P elements ( Drosophila)
 chaplerbi.DNAReph.cat#
DNA must be replicated prior to each cell division if each daughter cell is to the
receive a
copy of
•

genetic info By what mechanism is this DNA molecule replicated ?

.

3pwposedmechanismawiaionconse.ru ative Dispersive , Semi conservative

-

Conservative
•

x X ✓ •
Semiconservative
Both original strands The 2 nucleotide strands
- -

in
stay together in the the original DNA strands separate
new DNA strand & each serves as a template for
WRONGS the synthesis of a new strand .

All DNA replication is semi conservative .

CORRECTS

Dispersive pieces of
•
each strand is used for the template of the new strands WRON④

* Me sets on & Stahl demonstrated that DNA replication is semi conservative ( using equilibrium density gradient centrifugation)

/ /
✓
After 1 round of

AI
:÷÷÷÷÷÷÷÷÷:÷÷÷ ÷:÷÷÷m÷÷÷÷
:
:
replication, the DN

:s÷:÷÷÷a÷
s
DNA aombaaonatnatnaa been
'
SN
grown on medium
containing
appeared as a single band
 Thetatheplicatioh
•
: ( plasmids)
a type of replication common in bacteria & other organisms posses ing circular DNA

↳ generates intermediate structure that looks like Greek letter Theta ( O)

old DNA
•

Grey :

•
Red -

-
new DNA

(a) ( b) ( c)

( d) ( e)

d Double stranded DNA unwinds @ the Originofteplication templates in which

producing single strands that serve as
-
.

new DNA will be synthesized .

b. A ReplicatiOhBUb forms ( Loop w/

.
a replicating @ each end)
UPOxfam
ukepdinah : the point of
unwinding ,
where the 2 strands separate from the double stranded-
DNA he lil
* unwinding can occur at one or both ends of the bubble

itself -0 produces 2 circular DNA molecules each consisting of

C .
DNA replication occurs as the strand unwinds ,

one old & one new nucleotide strand .

•
Riollingfirdetleplicationi another form of replication used by some viruses & plasmids ( ex F factor)
.

I A break
.
occurs in one of the nucleotide
' '

strands , 5 d 3 end
creating a

2. New nucleotides
'
are added to the
broken
exposed 3 end of the
( unbroken)
strand, using the inner
strand as a template

are added
3. As nucleotides '
'
the 5 end
to the 3 end ,

displaces from the template

& creates a strand of linear
DNA

double -

4. Cleavage releases a

stranded DNA & a single

-

stranded linear DNA

which circularize &
may
serve as a new template
for synthesis of a

strand
complementary

* Produces multiple circular DNA molecules

linearI-uka.NO#RepicaHon
•
:
replication occurs @ multiple origins of replication simultaneously

•
At each origin of replication ,
the DNA unwinds & produces a replication bubble
•
Replication takes place on both strands simultaneously at each end of the
bubble , WI the 2 replication forks spreading outwards

When the replication forks run into fuse

one another,
they together to
•
create a

long strand of linear DNA

•
products = 2 linear DNA molecules

yRepliconiworiginnp.io?an.ornePstiarasn#
Characteristicsofthetatdollinqcirdeo
livejournal.cat#

÷÷÷÷: ÷÷÷÷÷÷÷÷:÷
'
"

. . ..

Rolling 1 circular molecules 1

Circle Circular Yes 1 Unidirectional

linear molecule that
circularize →
many
may
circular molecules

linear
Eukaryotic Linear NO MANY Bidirectional 2 linear DNA molecules
-
 DNASynthes.is# Replication -

must be
synthesized to be replicated

RequirementsforDNArepticationlsynthesis.si
ng le
-

stranded template of DNA → double stranded

-

DNA molecule must unwind to exposes the bases that act as a template

•
d NT Ps → DNA precursor substrates ; raw materials to be assembled into a new nucleotide strand

* d NTPS contain a deoxyribose sugar

& a base attached to 3 phosphate
groups

* New DNA is synthesized from

deoxy ribonucleotide
( d N TP
tri phosphates
s )

•
Primer → RNA primers are
synthesized by primase ; DNA Polymerase can NOT start WI out primer
•
DNA Polymerase →
synthesizes DNA molecules from d NT Ps ; catalyze addition of nucleotides

•
The new strand is
complementary & anti -

parallel to the template strand -

•
The 2 strands are held together by
bonds bln the bases ( red
hydrogen -

dotted lines )
A phosphodiester
In replication the ,
bond forms
the 2
' b In
3 OH group of the
-

nucleotides
last nucleotide
f
on

the strand attacks the

5
' n
-

phosphate group v

d NTP
of the
incoming

/
7

2 phosphates
are cleaved

[
off

Nucleotides Added to
'
3 -

OH group of the new strand

Directionofpeplication '

3 ( nucleotides
by DNA Polymerase)
' '
-

ALWAYS in 5 →
added to 3 end
' '

Because 2 template strands are antiparallel & DNA synthesis is →3 DNA synthesis
always 5
-

proceeds from right to left on strand I left to

one the other right on

IFFLEY Magog! ng Strand)

•
DNA synthesis
( a) strand
is continuous
-
on one
direction a synthesis
1- other
Of DNA & discontinuous on the

template strand exposed

'

Initiating I'alias >

Leadingham the
in the 345 ' direction Undergoes continuous .

replication ( new antiparallel strand synthesized

direction)
'
in
'
5 → 3

( b) >Laggingstrandi the template exposed in the

in
5) → 3 ' direction Undergoes replication
.

short
,
discontinuous bursts .

2. On the upper template strand, DNA synthesis

(c)
fork &
begins @ the proceeds in the direction
opposite that it out
of unwinding , so runs of
template .

b. DNA synthesis starts @ the fork

again on

upper strand ,
time
the
from the fork
each
proceeding
away
.

•
OKaZaKiFragment Short fragments of DNA produced by discontinuous synthesis
•
later linked together
by DNA ligase to form a continuous strand
•
have an RNA primer to start DNA
polymerase replication
 Bacterialkeplicationl
-

.
Initiation
↳ Deane Activation protein that promotes DNA
unwinding
:

2.
Unwinding
↳ DIA Activation protein that promotes DNA
:
unwinding
↳ DNAHeli separates the 2 annealed strands

S#BindMB)PNei :
stabilizes the single stranded DNA
-

during transcription
4DNA# :
unwinds DNA R relieves torsional strain
↳ Prima attaches RNA :
primers
3. Elongation '
↳DNAPoseHI Elongates :
( synthesizes) new DNA strand from the 3 -

OH
provided by
the RNA primer

↳DNAeraseI Removes RNA primers & replaces them w/ DNA

:

↳DNI DNA Polymerase I

Ligase repairs ( ligates) hicks created
" "

by
:

4. Termination
↳Tslteminahizaionsubtana.uaIts helicase can 't continue
so transcription

yDmNeAoYingYinnds@o.H wohwencaine.ca#eisregliucgiem.evgnszgpgin
.

the DNA ?
-

firing new origins of replication

C beofmreneEEsxiginengomeesregre.ae:9 have
forks meet together they,

already had a portion of their

p¥
DNA synthesis the DNA replicated
of
.

lagging strand -

The cells effectively

daughter

\
discontinues ly is
inherit DNA that only
in the direction opposite
that of partially replicated
unwinding
.

At each fork , DNA synthesis of

the leading strand proceeds continuously
in the same direction as that of
unwinding
 \
Continuous DNA synthesis begins @
'

the 3 end of the

# broken nucleotide strand

'

AS the DNA molecule unwinds ,

the 5 end is

progressively displaced

✓ produces a series of replication bubbles (

similarrepto.ca/Y.fenta)

Leading strand synthesized

continuoSly in same
direction

unwinding
as
y
that of

\ Lagging strand synthesized discontinues ly

in direction opposite of unwinding
Roles of Helicase , Gyrase , Prima se

Helicase binds to the template @ replication fork and in

•

lagging strand each moves

-

5
' '
3 direction bonds A moving the
→
along the strand , breaking hydrogen
replication fork

•
Gyrasei DNA gyrase relieves strain ahead of the replication fork
'

Prima synthesizes 3 Ott group to

short stretches of RNA nucleotides , providing a
-

which DNA Polymerase can add DNA nucleotides

Roles of DNA Polymerase III , DNA polymerase I , & DNA Ligase
⑧ E .
coli has 5 known DNA Polymerases
 DNA
Replication
Fork in

E .
coli

r •
The lagging strand template forms a loop so that replication can take place on

2 antiparallel DNA strands

•
Each active replication fork requires 5 basic components :

I .
Helicase → unwind DNA

2. SSB Proteins - & prevent

protect the single nucleotide strands
secondary structures

3. DNA Gyrase → remove

strain ahead of replication fork
'

4. Primase → 3
synthesize primers w/ OH group @ the
beginning each
-

a
of
DNA fragment .

5. DNA
Polymerases synthesize the leading &
lagging nucleotide strands

•
TerminationofkeplicationinE.co#
<
in some DNA molecules , replication is terminated whenever 2 replication forks meet

proteins (Tus in E coli),

L bound
in other cases, termination sequences by terminator .

blocking helicase activity , so replication halts

Thefidelityofreplicationishighduetoseveralfac.to#
•

The high accuracy of nucleotide selection

by the polymerase during elongation
-

proofreading ability Polymerase

-

of
↳ DNA III the 3 's 5
Polymerase
'
can excise bases in direction to remove
OH w/ in the
'
incorrect nucleotides sensed
, by altered placement of the 3 -

Polymerase then inserts the correct nucleotide

enzyme complex .

Mismatch Repair
↳ This mechanism relies on removal Of one strand of incorrectly paired
segments , & the incorporation of the complement of the remaining strand

EuKaryoticDNAReplicah
Differences in eukaryotic chromosomes require some differences in the replication process :

L
Multiple origins of replication
L
Licensing of replication origins → prevention of multiple origins of replication in a single gene so
you don't get multiple portions of replicated DNA
<
Mainyu forms of DNA Polymerase
Nucleosomes are quickly assembled onto newly synthesized DNA

• After replication , the new reassembled Octamers

are a random mixture of old & new histories