"I ↳

-5
5S

Bio 101
 ch3
-
concept -> Chemistry of water
&

* We can trace water uniques behaviour to structure and

interactions of its molecules
↓
shaped like a V two atoms
it is
to one atom
-> I
by drogencovelant are
bond
joined
oxygen by a
single
than
oxygen is more
electronegative hydrogen ,
so the electrons
covelant bunds spends time near
in more
oxygen
* These are Polar Covelant bonds]]
E this unequal charge distribution and water's v-shaped
make formolecule
it a

. 3
The
oxygen hydrogen is
is
cartially
I
neg ative S -

partially
Positive S I
xThe properties of water arise from attraction
between
↓ opposity
charged molecules .

The
to partial y positive hydrogen of
of one molecule is attracted

partial y negative ↓
oxygen nearly molecule
a

Held togather
by awagen bond
- When water is in its liquid form hydrogen bond are
,

vary ragile ,
to as
strong
covelant bonds
as

and reform with great frequency Each last only

Theyfewbreak
trillionith of second but molecules
.

a a are
constantly forming
new bonds with a succession of partners

coverlant
en bonde
-

-ge en
-
-

-
 Concept
32 Four
emergent properties of water contirbute to
Earth's forlife
Suitotabimoderate
lity temprature expansion
Cohesive behaviour ,
ability ,

upon freezing versitility

, as a Solvent

water molecules close to each other of

*
stays as a result

hydrogen bonding-- linked by multiple hydrogen water bonde we

more
Structured

hydrogen bond that

than other
Cohesion holds the substance

I
:
liquids
togather
result of cohesion due to
as a
hydrogen bonding us high
surface tension
-

-of how difficult to stretchor break the

measure it is

Surface of aliquid

S at the air-water interface is an ordered arrangement of

water molecules
↓
,
hydrogen bonded to one another not to air above

This asymmetry water an

usually high
surface tension
gives
 A Cohesion Contirbutesto the transport of
waterand other dissolved nutrients in plants
against gravity
! water from
.

roots reaches through a network of water

conducting cels.
water evaporates from leaf
as a
,
hydrogen bondfurther
Cause watermolecules
leaving the
down and upward Pull is transmitted
vien to
tug on

through water conducting cels all the

down to roofs
way
adhesion of substance to another -> helps
:

-clinging one

counterthe
downward Pull
-

-
-

-
-
-

of gravity

are nee
·
water absorbs heat from warmer air and releases heat
to cooler air" with tempreture"
only a
slight change in its own

Akinetic energy of motion <the faster a molecule

energy
:

moves the Kinetic

greater its energy)

Athermal Kienatic energy associated

energy with the random
:

movment of atoms

* Temprature average Kienatic energy regardless of

:
-

,
volume

A heat Thermal
:

energy
transfered from one
body of matter to
another

calorie amount of heat it takes to raise the temprature of

ly
: -

of water by PC
kcal =

1 , 000 cal
specific heat : -
amount of Cal =

4 1845
-

,
15 =

0 .
239 cal
heat that must be absorbed
lost for lg of that substance to
change
tempretuve
or its y
 of the
Because high specific heat of water , water will
4 change its tempreture less than other liquids .

we can trace waters

to hydrogen
high specific heat
heat must be absorbed to break-
bonding
down hydrogen bonds by the same token
;
,

heat must be

released when hydrogen bonds form

I

I temprature]
· moderate air tempratures stablize ocean

· resist changes in
organisms temprature

heat of vaporization->
a liquid must abork for ofthe wantine teacher
Ig
liquid to gaseous state

water's heat of vaporization

high results from
strength of its hydrogen bonds
evaporative Cooling : -

when molecules with most

kienatic energy leaves as
gas
I fl o ati n g
water is less dense
of Ice on
liquidagus solid
as a than as a liquid
at temprature
above 7 water behaves like other liquids,
as the temprature falls water to freeze, at O
begins
the molecules becomes locked lattice
in a
crystalline
·
suitability of environment for life
·
allows life to exsist under frozen surfaces in water bodies

Iwater The Solvent of Life I

:

* Solution :
-

a
liquid that is
completly homogenous mixture of
two or more substances

* Solvent :

dissolving agent
of a soultion

* Solute substance that dissolved

:

is

solution which water dissolved in water; water is

*
aqueous : -

one in is

the solvent .

↳
water is versatile solvent due to polar covelant
avery
bonds
 example/Nact placed in water->

The oxygen of water have partial

negative charges it's attracted
: so

to soduim cations
,
hydrogen regions
are
positivly charged and attracted to
choloride
animus
:
as a result water molecules Surround the individual
Soduin and Choloride them andsheilding from
ions
superating them each

other

hydration Shell : The sephere of a water molecule around

each dissolved ions
a compound
08
O 08 ⑳
0
does not need to
0 soO
0

0
O
Cl 0
0 Nat 0
·
O be ionic to dissolve
0
⑳ Do
o
in water
(Polar non-ionic bonds

like sugar dissolve in ,

water
:
hydrophil
water
i c -substance: that has an
affinity of

& a substance

water
can be hydrophilic
Cotton
without
actually dissolving
in

hydrophobicformsubstances that
·

are nonionic and non polar

:

that cannot bonds my

hydrogen veg oil

x Molecula mass : the Sum of all masses of atoms in a

molecule

* Mole : -

exact number of objects

molarmass= - 3/mo

Molarity -
number of moles of solute per lifer of solution
 -
-
-

-
-
-

break/stretch
difficult
surf in
it to
measure of
is
how
->

O -

~
v

0
 *
0
x

⑦
-
⑦

⑰ ⑦

⑦ ⑦
 polar covelant hydrogen
covalant
->

hydrosen

-> adension

-> cohesion
 Macromolecules ->

large -
complex molecules
Carbohydrates , protiens and Nucliec acide

Polymer : a
long molecule consisting of similar
many
-

building blocks

units that
monomers
repeating serves as
:

blocks for polymers

building

IEnzymes
up chemical
are specialized macromolecules that speed
reactions
I
within
example
- our
body
dehydration synthesizing reaction
a
polymer
hydrolysisbreaking digestion
down a
Polymer
when two monomers bond when polymers are
together through the ↓2assembled to
monommer
loss of a water molecule (reverse of dehydration)

HO I 2 3 H Ho H
HO 1 -4 H

S
H0
Fizo W
↓H20
H Ho-D-R--H Ho-- H
1 2
-

-
-
3 n -
 of
Diversity Polymers
·
a cell has thousands of different
Macromolecules
it varies the cells of organism , within
·
among an

a
species and even more between species

huge variety of can be built from

a
polymers small
·
a

set of monomers

concept 5 2 Carbohydrates Sugars and polymers

:
.

,
of sugars
CnHenOn n- number of Carbons

· Simplest carbohydrates are monosaccharides

or
simple Sugars
8
Carbohydrates macromolecules are polysaccharides
composed of many sugar building blocks
Monosaccharides have molecular formula that
are multiple of the unit "CH20"

Trademarks d Carbonyl group

:
=

c =
0

*
hydroxyl group-OH
.
·

classifying Monosaccharides : -

1) location of
is either a ke/carbonyl group , a monosacarid

2) The size of the Carbon Skeleton

from
Cranges three to seven carbons]

* another source of diversity for simple

Sugars ,
the
way
their parts are arranged
spatially around aysumetric carbons
 it's to draw
Although convenient glucose with a

Skeleton it accurate
linear carbon is not
completly
C in aqueous soultion five and six -

carbon sugars form rings because they are

the most stable form of these sugar

Monosacharides
/ ↳
major fuel for raw material
cellular work for synthesis
of other type
of organic
molecules (fatty +
amino aecids)
 disaccharide -> two monosaccarides joined
together through glycosidic linkage a
a ,

covelant bond formed between two monosaccharides

-

by a deby diration reaction .

1 ,y
glycosidic
linkage
·

-
oseXse ose -

&
cose x ose e
- -

linkage
·

sexose
Lactose
3 -

Disaccharides must be broken down

into monos accrides to be used as
energy
 glycosidiccarbon
linkage
O
I

joins
carb
mo

-
↓

forms a five sided

ring even
though its a

hexoses .

lactose intolerance

-
common condition in humans

wholock
glucose
tase:theenzyme tatee
galatal

broken down
sugar is

bacteria .
by intestinal
 polysaccharides polymers
-> of sugar with

storage and structural roles

· The architecture and function of a polySacchride

①
determined by its monosaccharides and the
position of glycosidic linkages & .

/storage polysaccharides]
startchy a storag e polysaccharide
of plants consists of glucose monomers
↳
synthesizing startch enabels plants to stockpile
surplus glucose

lucose monomers startch

39 -Y
in
a
glucose)
 Most animals including humans also have that
, ,
enzymes
hydrolyze plant startch ,
making glucose available as nutrients

(forPotato
cells

tubers fruits
, of wheat , corn , rice are major source of
Startch in human diet

form
-Simplest
of
Startch
->
- -4 linkages

-- -Glinkages
2

-
C
animalstorage

B
·

Simplest form of startch is

amylose
"un branced
startch with
:
anylopectin a more complex 1-6
linkage

glycogen-> storage
a
Polysaccharide
in animals liver and muscle cells
->

↓
Breakdown of glycogen releases glucose when
demand of Sugar increases

tensively branched intrudereaunits

the ex
function rail
 [Structural Polysaccharides I
Ethe
Polysaccharide cellulose in a
or

Compenent
like startch it with 1-y
is a
polymer
with a different
glycosidic linkages but
ring structure

-
Gurgiul straighte
* Cellulose is never branched
6
some hydroxyl group hydrogen bond with the
hydroxyls of other parallel cellulose molecules
*
Enzymes that digest startch by hydrolyzing
a linkages Can't
hydrolyze /3 linkages

A "insoulble Fiber is cellulose

*
Some microbes use
enzymes to digest cellulose
x
many herbivores
from cows to termites have
symbiotictel,
with these microbes

Chitin-> structural polysaccharide found

in arthopods exoskeletons
: its also found in
fungi which uses it as
building
material for their cells
I
the
13-glucose monomer of Chitin has
a
nitrogen-containing attatchment
concept 5 3 - .

lipids large biological

->
molecules
that does not include true
polymers
↳
They are
grouped together because they are

all
Chydrophobic
·

although they may have polar bond assiziated

0 with
consists of
oxygen they ,
mostly hydrocarbon region
with
relativly non-polar CH bonds

Fats - consists ofaglycerol molecule

joined to three
fatty acids
-
glycerol
alcohol
is an
each of
fatty acide
its three carbon
long carbonattached to
bears a
hydroxyly Skeleton
group rup
Carboxyl I
↳givesTheseMoleculeie
-

->
So Synthesis
fat
of one

mole call
- -

requires of
-

- removal
3 water
molecules

triglyceride
triacylglycerol
.
The relativly non-polar <-H bonds the hydrocarbon in

chains the these fats

is reason
my ↓ w
hydrophobic are

fats separate from water because the

water molecules
other and exclude the fallydrogen bond to each

each
fatty acid is joined to a
glycerol by a

-
denaration reaction resulting in an easter
X I linkage
tri acylglycerol
Bond between
triglyceride
a
carboxyl and hydroxy
group
*
fattydifferent
three
acids can
kinds
all be the same or of two or

Saturated
of
fatty acid
possible and
-
maximum number
double bonds
hydrogen no

unsaturated
more
fatty acids - has
double bond with one fewer
,
a one

hydrogen atom
or
on
each double-bonded carbons
I
normally a cis that creates
bond a
kink thein
hydrocarbon
-
L

saturated unsaturated

"stable and lightly

↓
The Kink
Packed that's why prevents the
in room tempreture molecules from
it's solid being packed it'sthat's
liquid
in
whyroom temp
 · a diet rich in saturated fats
may contribute
to cardiovascular disease called atherosclorosis
through plaque deposit

Hydrogenation -> process of converting unsatural

fats to saturated
by adding hydrogen
↓
hydrogenating veg oil creates unsaturated
fut with ble bonds

coronarydisease
heart

Major function of fats is to Astore energI

Cagram of fat stores morethan twice
as much energywe lsawie
e

Mammals store their

long-term food in

adipose cells
* adipose tissues also cushions vital
organs
 0
*
X

I -
at O
!
dir
0 2
-
olt
0
=
OH
or

-- c
-

=
C
- c
d↑

- -
-

-
not a ll
X
-

-
·

an
-

~
0

X
X
X

0 -Kind
 Similar to fat molecule but
phospholipfatty
ids
two
->
acid and a
glycerol
a
,the third
hydroxy/group
group isattatched to a ⑱hat
P
C

negat i ve
-

Typically an

polar molecule
additional
is
small
linked to
charged
a
or

phosphate group
"has
-charg e
a

a choline for example .

The two ends of Phospholipids show different

behaviours with respect to water hydrophillic
⑧
mech .

->

&⑤↳hyde
e

Hydrocarbon tails are hydrophobic ande

·

execluded from water

NHS
and its attatchment form
·

phosphate group ↑
a

hydrophillic
water
head that has an
affinity for -p =o

↓
glycerol- C-CH2
->
I
H
H2

fan) is s
 choline

I
Pr
-

&
glycero &

↳ easter
linkase
phosphatidyly choline

M
 when Phospholipids added
to water

are self-assemble
double layer called bilayer
into

S
PThe hy drophillic head are outside the bilayer
D hy drophobic head points toward the interior
of bilayer
A bilayer forms a boun dary between cell and
-its external environment-----
Steroids > lipids characterized by
carbon Skeleton of four fused rings

cholestrol of steriod , crucial molecule

in animals ,
:
type
-

component of animal cell membrane

and Precursor from which other steriods are
synthized > synthized in liver and obtained are
C high levels contirbute ↑
-
to atherosclerosis
I-
may
HO/ /I
↳
 Concept 5 4 -> Nearly every dynamic function of
.

a
living being
S
depends on protiens
they account more than So x of the dry mass of most cells

Enzymatic Protiens regulate metabolism by acting as

catalysts
I
.

chemical agents that

selectivy
reactions without being consumed
speed up chemical

ahuman has ten of thousands of different

Protiens each with a specific function and structure
,

I
each
type of protien have a unique three
dimensional shape

all protiens are Constructed of the same set of

co acids linked in unbranched
polymers
· The bond between amino acids is a

peptide bond a
 a
polymerof amino acids ->
Polypeptide
Protien biologically functional molecule made
of each foiled
up one
into a specific
or more
polypeptides
three dimensional structure .
,
and coiled

Defensive Protiens
①
Enzymatic Protien ②
Efunction protection
Sfunction :
selective acceleration ex/
: -

against disease
antibodies
,

of Chemical reaction
ex digestive protien
④ Transport Protien
↓function :
-

transpor substance
O Sstorage protiens
3 ex hemoglobin
function sLove amino acids
..

ex/casein (milk) ,
ovalbumin
(199)
⑤ hormonal protien ⑥ receptor protien
S
Sfunction -coordination of
: an function :
Response of cell to

organism's activity Chemical stimuli

exinswin ex/receptors built in the membrane

of a nerve cell detect signals

⑦ contractile and motor ⑧ structure

↓
I Protien function : -

support
function motion ex Keratine
ex/myosin ,
activ Collagen
das tin
Amino acids
organic molecule with
an
both
- group and aC
-
an amino carboxyl group
S
at the center of an amino acide there's
carbon atom cal led
aysmetric R

carbon
IO
C- C
S N -

OH
its four parterners are
i
an amino group, a
carboxy group
atom ,
a
hydrogen a variable group (side chain)

I differs with each amino acide

physical and chemical properties of the

side chain ,
determin the unique chantastics of a
Practicular amino acid

Piney are grouped according to the charatrastic

of their side Chair I ⑰
- ↓ I ⑦ basic
non-Polar Pola& acidic
↓
hydrophobic it
 Ateptide They range -> in
length from few
acides
a
amino
to
1 1000

when two amino acids are positioned so that the

carboxyl group
of one is adjacent of another
to aminog roup
reaction ,
,
they become

joined together by dehydration the resulting is

bodde
a Polypeptide E

repeating over
of
and over the process
,

amino acid linked

yeilds a
polypeptide
a
polymer many by a

peptide bonds
R
H
-
↑ /o
-
C-
A
-I WOn C
N-termines
epeating
terminus

sequence of
atoms -> backbones
 Structure
the
Polypeptide
-from Pr the

Protien Structure
C The
and
&
function -

·
specific properties of protien results from their
is
intricate three-dimensional architecture

* The term
polypeptide is not
synonymous
with the term protien

functional Protien is not just one

polypeptidetwisted
chain ,

but one or more poly-petides precisely folded ,

into molecule of s hape

a
unique .

S
Thi
fol d i n g
the formation of
is driven
various
and reinforced
bonds in
by
chain , which
in turn depends on the
sequence of amino acids
↓
A protien specific structure determines
how it works
,
it depends its ability to
on

recognize and bind to some

other molecule
protiens can be represented in
different
ways depending on goal
the
of illustration .

L
V
W

Space-fil
"Emphasizes
ling model Ribbon model
-
shows
I
wire-frame
the overall
only
globular shape" the
polypeptide shows polypeptide
backbone backbones with
side chains
extented from it

trans
↳
pert shape) (solid shape)
6 structural details
show the shape as
well as some internal are not needed

details
 Four levels of protien structure

①Primary structure ->

sequence of amino acids
↓ ↳only peptide bond
The precise structure of protien
primary
is not determined by random
linking of amino acides but
inherited genetics

② secondary structure - Coils and folds in the

repeating constituents of
polypeptide backbone
within the backbone
oxygen atoms have partial
,
the
Nitrogen
attached
to

negative charges ,
and the
hydrogen atoms have partial
positive charges i therefor hydrogen bonds form
↳ these bonds weak because they are
individually are ,

repeated many times over a relativly long region of

chain
polypeptide they can support a Protie
praticular shape
 E

delratenten
two
of
or more
segment
polypeptideside chain
laying sidebly
between
every
fourth amino acid
S
ex) A heratin
③ Tertiary structure -f overall shape of a
polypeptide
resulting from interactions between R groups of various amino

acides
V ↓

hydrogen
↳

hydrophobic and ionic bonds disulfide

between tue
55
Van der waals
-
59 bridge
bonds between and-ve
charge side
Polar side chains
④ Quaternary structure overall structure that
-
results from the of these
aggregatio polypeptide subunit
ahelit
↓ ↓ 2
-Pleated
collag
- 2B
sheet
hemoglo bin
->

en
transthyretin ↓
↑
3 polypeptides
C
-
↳identical

so
polypeptides

norpolyopeptide
mponent
any
With atom
ironthat binds
gen
 Sickle-cell disease -> A structure
I change in
Primary
⑪ Even a slight change in primary structure can affect protiens
shape and to function
ability .

Sickle-cell disease :
inhertied blood disorder , is caused

by the substitution of one amino acid Cualine) for the

normal one (glumatic acid) at the Position of Sixth anino

acid
E
RBC
into
agregate
a sickle shape

what determines a
protien structure
addition to structure
in
primary
[Physical and Chemical Condition]
↓
Eempreture
X
PH

denaturation
salt concentration

loss of
-
native
: -

a protien's
structure -> in active and in functional
Protien folding in the cell

Misfolding of
polypeptides is a serious problem
7
-
madcow
cystic fibrosis Alzheimere Parkinson's disease

it's not eas to determine the exact three

y structure
dimensional
↳

S I
⑯
X-Ray crystallgraphy
-Nade
A
is
diffraction of an
↓
ene
beam by the atoms X-ray
of
a
crystallized molecule

-
electr
cyromicros
om By
Col
* Bioinformatic

N -
some protiens do not

have a distinct 31 structure

until they interact with

target
protien or other molecule
↳
"intrisically disordered
protiens"
concept 5 5
.
-> Nucliec acid store transmit and
, , help
information
express heredity
X The amiono acid
sequence of polypeptides is
programmed
discrete unit of
by a inheritance known

ere
genes consists of DNA which belongs to the
class of compounds called nuciec acide

made of
· Nuclic acid
-Polymers
called nucleotides
:

-
monummers

↓ -
deoxy ribonudiec acid ribonucliee
Acid
"DNA"
-

"RNA"

enable living organismsreproducethe ent

 · DNA provides directions for its own replication
·
Direct RNA
synthesis
control
protien through RNA
synthesis
·

gene expression
from
& DNA is the
genetic material that orgnasims inherit
their Parents
& each molecule
chromosom contains one
long DNA ,
usually
several hundred
carrying more
genes
or

when a cell reproduce itself by

from
dividing ,
its DNA molecules are

copied and passed one generation to another .

3
a
given gene through DNA molecule
can direct synthesizing atype of
RNA called Massenger RNA

R
unti
L croter W
mRNA
ma
interacts
I
with protein's
"Central
dog
synthesizing machenariy
to direct synthesizing polypeptide
·
The sites of Protien Synthesie
are cellular structures called Domes
↓
pin eukaryotic
but DNA resides
cell ,
ribosomes
nucleus
are in
asi
in I
↓ region between
MRNA
conveys genetic instructions nucleu and cell

for
building protiens from nucleus outer boundry
to
cytoplasm

A Prokaryotic cells lack nudie but still use

MRNA to convey a message from DNA to
Riboseme

Nuclic acids are Macromolecules that exsist

as
polymers called
polynucleotide
L -
W

Pentose nitrogenous pentose

sugar
Sugar base C->
nucleoside
 The portion of nucleotide without any phosphate
group- nucleoside
used to build a polynucleotide
thebeginningphosphate
monomer
but two are last
groups ,

through polymerization reaction

--

-
nitrogenous base !
-
- - -

pyrimidine purine
Ehas one ↳

I Nin
six-membered membered
ring fused
six
of carbon and to a five membered
ring atoms
ring
nitrog en
WHz 0
11

-
-/

I Guanine

xRy/Ree,Y
N

- L
N
H e

cytosthe Adenine
110
L Y
11
L ↓
·*
/
HN C
C
1

/
·
DNA-
on the Second
deoxyribose
Carbon
m lacks an
oxygen atom

·
RNA- ribose vo
one to

& three phosphate

I groups are attach
to 5'carbon of the sugar
e n
e -

The
linkage of nucleotides into
condensation
polynucleotides involves a

reaction H

adjacent nucleotides are joinedby

a
Phosphodiester linkage
phosphate group covelantly
C

links the of two nucleotides

sugar
sugar-phosphate units ->> sug arphosphate
backbones

* The two free ends of

different polymers are

distinctly
X ⑧ -
Phosphate a
hydroxy /COH)
attached to
5'carbon group attached
to 3'Carbon

⑧
 structure of DNA and RNA

DNA RNA

has two
·

that wind around

polynucleotides ·

Strand
exsists as a
single
an
imaginary axis
forming
are helix ·
complement ary pairing ofcan
occur between regions

sugar Phosphater
·
Two two RNA molecules , or even

run in different 5'- 3 stretches of nullitide in the

direction
. anti Parallel] same RNA-> allows it
to take on Praticular
· Two strands three dimensional shape
necessary for its function
heldby hydrogen
between paired G +RNA
bases
A -

T c -> c · Adenine Pairs with

two strands are Ura cil
U
complementary A -

↳
this feature makes it ·
RNA may have PreceededDNA
to genrate two
possible of DNA
identical copies
 Cell Structure and function

Concept 7 1 biologist use

. ->
microscopes and
biochemistry to study cells

Light Microsca(M) : -

visible
light pass
lenses
through
the specimen then
through glass
.

The lenses refract (bend) the light so that

the
image is magnified .

Ihrezimportant patters
-

of
microscopy : -

①magnifications Natio of objects to its real

⑯ image size .

& Resolution measure of clarity of the distance

image
:
, minimum
of two distinguishable points .

③ Contrast: visible - differences in brightness between

parts of the sample .
 10
->
100 -> 10

mote lox Objective = Ocular

Lens lens

*
light microscopes can magnity effectively about 1 000 time the
,

actual specimen Size .

* enhance contrast -> stain or Label Cell Component

A the resolution of standard light too

microscopy is

low to
study organelles
-
~

C
C
=
-

a
a

~
it
1 1 -,
je -

- -

(Normarskil
Bright feild -> Differential inference contrast ->
·
light passes directly
- - =
exagrate differences
·

-
in
density
specimen Most
th ,
image
-
almost appears 3-1
---
-
.

stains require cells to be

-

Preserved which
e
Is them
· Phase contrast : -
Variation
-

intensity within ustained -

to enhance Contrast
specimen
-
-

all imp for-

-

in unstained cells the ,

living cells
fluvoscence -> Confocal uses-
laser to -

location of specific
- -

amoffluvoscene
Molecules are revealed
-

-
out
focuslight eliminated
-

by labeling
--
molecules with byturing sharinges at
fluroscent orantibodies , which different places , creating
-
--
sorbs avaidetation e 3-D
a much sharper
image .

--

Deconvolution -:restructed super resolution ->

imagesat
from
many indiafluroscent
different
-

- -
-

p laces digitally
,
-
ited
molecules

at
- and their position
re
-
light
eource -

rded,
->
,

info from ining

cre
mag a 3D e .

many
-
diff
places "breaks"
-

the
- - -

resolution
- limit . The

size
-
of each dot is well
-

-
below the 200 nM
-
-
 In brightfield microscopy, light passes
-

Describe the process of brightfield directly through the specimen. The image
--

That
microscopy. has little contrast and staining with dyes can

passes
-
-

light
enhance contrast.
-

uses
it can be stainc
through specimen ,

What is the purpose of staining in Staining with dyes enhances contrast in

microscopy? microscopy.

contrast
enhancing

Confocal microscopy is a type of

fluorescence microscopy that uses a laser to
Define confocal microscopy. create a single plane of fluorescence,
eliminating out-of-focus light from other

E
uses user to
creat
planes.
-

enilimanting out focus of other planes

single flurcente plane
a +

of

Phase-contrast microscopy amplifies

How does phase-contrast microscopy -

variations in density within the specimen to

enhance contrast in unstained cells? -

-
enhance contrast in unstained cells.

implifying variation in

density

Deconvolution is a process where many

Describe the process of deconvolution in blurry fluorescence images at different
microscopy. planes are reconstructed to create a sharper
image using deconvolution software.
out of
digitally remove
focus light and reassigen it to its source
 Differential interference contrast microscopy,
also known as Nomarski microscopy,
What is the purpose of differential
enhances contrast in unstained cells by
interference contrast microscopy?
amplifying variations in density within the

Creat a 3Dimage specimen.

by exaggatrality density

Confocal microscopy allows for capturing

What is the advantage of confocal
sharp images at many different planes,
microscopy over standard fluorescence
which can be used to create a 3-D
microscopy?
reconstruction of the specimen.
out of focus light in

standard flurescence microscopy

is not enliminated

Confocal microscopy uses a laser to create a

How does confocal microscopy eliminate out-
single plane of fluorescence, eliminating out-
of-focus light?
of-focus light from other planes.

creatine "
"

avoscene

Describe the process of digitally removing The process digitally removes out-of-focus
out-of-focus light in phase-contrast light and reassigns it to its source, creating a
u?
microscopy. much sharper 3-D image.

in
Iwrong
deconvolution
question

What modifications are used to exaggerate Modifications are used to exaggerate

differences in density in phase-contrast differences in density in phase-contrast
microscopy? microscopy.

optical
 Locations of specific molecules are revealed
How are locations of specific molecules by labeling the molecules with fluorescent

fluorescence
-

revealed in fluorescence microscopy? dyes

-
or antibodies, which absorb ultraviolet

by
radiation and emit visible light.
Labeling them -

or antibodies which
absorbs
is nie light
let light and
dye ,

What are the organelles called that appear The organelles called mitochondria appear
orange in the fluorescently labeled uterine orange in the fluorescently labeled uterine
cell? cell.
-nitochondera

DNA - blue cytoskeleton -> green

Super-resolution microscopy is a technique

that combines information from many
Define super-resolution microscopy.
molecules in different places to break the
- resolution limit and produce a sharp image.
UV light excites
Moleales offluroscence
 electron Microscope (M) :
focuses on a bear of electrons through
the specimen orinto surface
↓
resolution is
inversely related to the wave
length ofLight
↳ electron
[ have shorter
wavelengths]
electron microscopes (SEM)
Iscanning
useful for detailed study of the
topography of specimen
↓
Electron beam scans the surface of sample
coated with a thin film of gold The beam excites
.
,
usually
electrons on surface the
secondary electrons are
detected device that franslates signals of
by a

electrons
(EM)
Transmission electron microscopes -> aims an
electron beam
throug a
very thin section of specimen
 new developed type
cryo-electron Microscopy
↳allows specimen

E
disadvantage of SEM and TEMG to be preserved
at extremly
low tempretures
the methods Customarily to Prepare the specimen killthe cells
and introduce artifacts that do not exsist in cells
living

Recent advances in light microscopy

· flourescent markers improve the level

of detail that can be seen

·
Confocal and deconvolution microscopy providesharper
images of three-dimensional tissues and cells

· New
techniques forlabeling cells improve resolution .

·
super resolution allows one to
distinguish
structures as smalles 10-200m across
 ⑧
⑧
-
-

-
-

Cyro-electron Microscope a a new

type of
! to be preserved
TEM

E
allows specimen
at low tempratures This
extremly .

specimen of tissues or
avoids the use of preservitaves , a
visualization of structures in their
l owing aqueous
protiens
solutionsof

are frozen
cellular environment at tempratures less

Mean creations
arePassed In reene
the molecule .
 cell fractions
takes cell apart and sep rates
the major organells and Subcellular Structure from
one another .

The peice of equipment that is used (centrifuges]

A At each speed ,
the
resulting force tocauses a

subetof thecomponent both

te the e

at lower speed->
larger components
-
waste
↑
nuclei and cellular debris

2 -
Mitochondria and Chloroplast

at higher speed -> Smaller Components

-microsomes
2 -ribosomes

& cell fraction enabels researchers to prepare

specific cell components in bulk and
identify their function
* Biochem and cytology help correlate functions with
structure
 Cells are homogenized in a blender

to break them up mixture is

-
·.J..
centrifuge
Pellet
- .

The
liquid above the is

Poured into another tube and centerfuged

at
higher speed .

- -

Concept 7 2
:

cells - basic structural and functional units of every

organism

- X I -
->-

:S
Prokaryotic .
Eukaryotic
-

: -
Bacteria Protists (unicellular
Eury
· ·

·
Archaea ·

fung ;

·
animals
·
plants
 Comparing prokaryotic and
Eukaryotic cells

All es Prokaryotic Eukaryotic

* Plasma * No nucleus * DNA is in an
membrane called
* DNA is concentrated
organelle
region not
eraned
in a

* semifluid closed called is

membrane

jelly like liquid nucleoid

Sol & within the cytoplasm
in spite of absence of organel suspended in the cytocol
formless of organells
Prokaryotic cells are not a are a
varity
Chromosomes
*

soup , it contain
regions
↳
carrygenes in
form of DNA
the surrounded
by protiens *
Eukaryotic
where specific reactions
tapae generally
are
much larger
Ribosomes_
makes protien
 Plasma membrane
e Selective Barrier that
allows sufficient passages of oxy gen ,
nutrients and waste
to service the volume of every cell .

* The smallest cells known are called

(KMycoplasmas]]] -diameter of andlum

* Typical Bacteria -> 1 -5 Mm

cells
*
Eukaryotic 10-100Mm

H
for each sequare micrometer of
membrane of
limited amount practicular
only a

substanc can cross per second

3 so the Ratio of Surface area to

Volume is Critical

A as a cell increases in Size, its volume

grows proportionately more than its surface area

 ratio of surface to volume
a smaller cell has a
greater area

I
largersmaller
organisms
than
do not
generally have
larger cells
org ansims -

ty simply have more cells

↓
a
sufficiently
Area to volume is especially
high ratio of surface
important in cells that

exchange a lot of matterial in its

surrounding such

as intestinal cells .
 structers
surface of some
&
on the

Prokaryote
ventioned where
- ->
regionDNA
↳enbraue is
located

outercoating of many prokaryote ,

Cons i fing of a casulor

C slime lay
&

)
locomototion of
organdle Someprokaryote
 Eukarytoic Cells
I
it has extensive ,
elaborately arranged internal membrane
,

that devide the cells into compartments

↓
.
cell'scompartment provide different environments that supports specific
metabolic function

* Plasma membrane and organelle membrane

participate directly in cell's metabolism because many
,

built right into membranes

Enzymes are .

H
The basic fabric of biological membranes is a double
layer of phospholipides
and other lipids .

However ! ! each
, type of membrane has a unique
Composition of lipides and suited
Protiens to that membrane's

specific function I
ex/enzymes embedded in the membrane of organelle called
Mitochondria function cellular respiration
in .
 -

335 5 .

-
S W
I
E
-

S-
Y -

↓gS j"W
S
> -

.....
S -
 Concept F3 .
-

The eukaryotic cell's genetic instructions are

housed in the cell's genetic instructions and are housed in the nucleus and
carried out by ribosomes
two celluarcomponents involved
genetic control of cell
in

* nucleus : -
houses most of cell's DNA
* Ribosomes : -

Uses information from the DNA to make protiens

*
Nu Fryfic Stan ment reiemerch , naria
and chloroplast)

# the most conspicuous organelle (about 5um in diameter)

5 g I
S, -

* Nuclear envelope encloses nucleus separating its

Contents from cytoplasm
↓
double membrane , each Consists of lipid
bilayer with ofassociated
20-40
protiens , sepratedby
a space nm
The envelope is perforated by pore structures that are

about loonm in diameter

* an intricate protien structure called a pore complex

line each pore and regulate the entry and exsitol
(Protiens RNAs large Macromolecules)
, ,

The nuclear side of the envelope is lined by

Inuclear laminal net like
array
of protiens
filaments called intermediate filmanets
that mentains the shape of nucleus

by mechanically supporting
nuclear envelope

Nuclear matrix -> a framework

of protien fibers extending through nuclear interior

matrix
O +

E
 -~
WA is to called⑧
discrete chromosomes
·
organize --

· Each chromosom contains one

long sociated
wit
prines
I
someothe protie coil the DNA
molecule of earmosome
-

B
aromatin the and Protiens
xo
making
:
-
Coil DNA molecule
up chromosom Protien
- ③
⑧ sociated
with
protions

①
3 organized
discrete
called
anromworme
into units

ente complex of
shromosome
protien and DNA making up

① cell not dividing ->

chromatin
appearas diffuse mass

② cell dividing -> chromoses

coils and loops
 is
· Aoulus :
-
a prominent structure within non deviding
nucleus --.

-
rRNA is
synthesized here
# protiens imported from cytoplasm are assembled with
~BNA into small and large ribosome subunits
I
The subunits exsit the nucleus through the nuclearlores to
cytoplasm , where a
large and smal subunits can beassembled
into ribosomes

Nucleus directs protien synthesis by synthesizing MRNA

I
MRNA transported to
cytoplasm
S
ribosome translate mRNA genetic
mess gar structure of a specific polypeptide
 Ribosomes : -

Complexes made of al RNAs and

-

Protiens -

No Ribosomes are not membrane bounded

- -

thus not considered organelles .

cells with high rates of protien

synthesis have praticularly
·

large number of ribosomes as well as nucleoli

↳ ex/pancreas which makes
many digestive enzymes
have a few million ribosomes .

<
2
bound Ribosomes
Free ribosomes C
(suspected in
cytosol)
attacheoutsid tie
(or nuclear envelope
a
↓ ↓
Function within into
pinsertion
cytosol ; enzymes membrane
that catalyze the first step Packaging within
of makingsugar & certain organels
(lysomes)
export from
& cell
tF4 .

-> endomembrane system regulates protien

traffic and preforms metabolic function

endomembrane
system many of different
:
membrane
bounded organelles of eukaryotic cells

↑
I Nuclear envelope The membranes of this
1 Endoplasmic reticulum
.

system are related either

-
1 golgi apparatus through physical continuity
El
lysosomes or
by the transfer by vesicels
Evacuoles
E Plasma membrane

Endoplasmic Reticulum Biosynthetic :

factory
I
-

extensive network of membranes that accounts formore

than half of the total membrane
many Eukaryotic cells
in

· ER consists of a network ofmembranous tubals and sacs

called Cisternat
 ER cavity
ne

=>

y
with nuclear
continuous
envelope

Smooth ER : outersurface lacks Ribosomes

Rough ER : -
studded with Ribosomes on the outersurface of
membrane

Functions of Smooth ER : -

->
from scratch
①lipid synthesis & metabolism of carbohydrates

③ detoxification of
drug and Poison ↑
storage of calcair
of Smooth ER important of synthesis of lipids
↳Enzymes are

Sexhormones and hormons secreted

by
↓
advenal glands
Testes and ovaries SS
are rich in

SmoothER
 other cells of Smooth ER
in liver cells
help
ity cells espically
I
adding hydroxyl to drug
molecules

example ->Sedative phenobarbital and other barbiturate

fact barbiturates , alcohol and other molecules

in

ce
many
the proliferation of Smooth ER
-

-2
I -
.
J's

-> if its abused it decreasethe effectivness ot dress

The Smooth ER also stores calcaim cons

in Muscle cells-
when a muscle cell is
stimulated by a nerve
impulse calcuim rush
back across the

ER membrane into
cytosol and frigger
contraction of muscle
cell
 functions of Rough ER
Secrete that
Many cells protiens Produced by ribosomes attached to
are

ER ; Pancreatic cells produce in ER and Secrete this hormone

into blood stream
as a
polypeptide grows from a
bounding ribosome ,
the chain is

threaded into ER lumen through a

pore

secreted Protiens
Most are
glycoproteins
Protiens with

carbohydrates covelantly
bonded to them
* after secretory protiens are formed
ER membrane keeps them seprate
from protiens
cytosi
in

they depart from

of
ER wrapped in
that
membrane resicals
S
bud like bubbels
Transport resicle -> reside in transit from one partof
the cell to another

addition to secretory
in
maki n g protiens Rough ER is

↳ it
a men brane
factoryof cells
grows in
into
place by adding phosolipides and
protiens its own membranes

* As
polypeptide is destined to be membrane

Protiens grow from

ribosome , they are inserted
ER membranes and anchored by
in
hydro-
phobic portions -

*
rough also makes membrane
ER
Phospholipides ↓
where is
Rough
ER abundant ??

secretory
tissues
 apparatus shipping and receiving center
Golgi
:

after
leaving ER many transport vesicels travels
golgi apparatus
,

Here -> Products of ER are modified

and stored and then sent to other destenation

↳ extensive
espically
for secretion
in cells specialized

Golgi apparatus consists of

associated ,flattened
a
group of
membranous sacs -> /Cisternae]
The Two sides of Golgi stack are refered to as

Cis face and transface

givegriseto
vesicels that
to other
travel
Sites
↑
O C

a vesicle that buds

C
face by fusing with a Partie
add its membrane and
from ER cancontent of its lumen to is
& products of endoplasmicriticula is
usually modified during transit from
is to trans

&
Golgi apparatus also manufactures some macro-

molecules
↓
Polysaccarides Pectin
->

like
=>
secretory protiensprotiens secretory products
, non

· made in the
Golgi will depart from transface
and fuse with the plasma membranes, the contents
are released and the resicels membrane is incorporated
with plas ma membrane increasing its surface avea
 E-- -

-
-

e n

until
recently Biologists
static structure,
viewed

golg; as a

model of
a new golgi was
given
a
dynamic structure
my According
to cisternal model
maturing ,

Colgi actually progress forward

from is to trans face,
carrying and modifing their caryo

as they move
 bysosomes :

Digestive Compartments

-
tha
of hydrolytieyes
membac -

letsee
↓
works best in acidic environment
inside
lysosome
Hydrolytic enzymes
made by Rough ER and
and
lysosomal membranes
transfered to golgi
then
are

apparatus for further processing

-
imp how are protiens of inner surface of lysosomal membrane
and digestive enzymes themselves are spared from destruction?
I
Answer/ The three dimensional shape of these
protiens protect vulnerable bonds from enzymatic attack
↓
once it exists it becomes active
phagocytosis -
"
25
-
autolThogy
↓- ↓
engulfing ancells lysosomes uses

I hydrolytic enzymes to
ex/white blood cells Macrophages
ethe
cell
-> a
↓
The food vacule formed
fuses
in this
,

way then
adamaged organelle
with lysosome becomes surrounded
a double membrane
by
and lysosome fuses
with the outer membrane
of this vesicle
↓

exhuman liver cell

recycles half of its
molecules each week
The cells of people with inherited lysomal storage disease
Lack a
functioning hydrolytic enzyme normally present in lysosome
N
The
lysosome
material .
becomes
engorged with indigestable
↓
disease = lipid-digesting enzyme
Taysacinactive a is

missing or the brain becomes

, impaired
⑪
I by
accumulation of lipides in cells y
51 rave in
genral population
vacuoles :
large vesicles derived from the endoplasmic
reticulum and golgi apparatus
A
integral part of endomembrane
system
like all cellural membranes , the vacuolar membrane
is selective in solutes : the solution inside
transporting
a vacuole differs in composition from the cytosol

① food vacuoles - in phagocytosis

& Contractile vacuoles y

i
*ess water from
-
-
cells ,
suitable concentration of ions and
thereby maintaing
- -
a
-

molecules inside
-
a cell
E central vacuoles is plant cells
develops coalescence of smaller vacules , The
by
Soultion inside the central vacuole is called sap,

es
-
-
-

of
main
repository inorganic
ions such as
randd
*
Plays a
major rule in plant growth , as the
the cell to
vacuole abosbs water,
enabling
become large with minimal invesment in
cytoplasm
often between central
& The
cytosol occupies a thin
layer
vacuole andplasma membrane , so the ratio of plasma
membrane surface to cytosolic volume is sufficent

exocytosis
mitochondria and chloroplast change energy from oneform to another
↓

Mitochoderia Sites of cellular respiration ,

: -

the metabolic Process that

oxygen drive the
uses to
generation of ATP by extracting energy from fats sugars ,

and otherfules

chloroplast found in plants and algae stes

of ,

Posynthesis
Endosymboint theory
similaraties with bacteria
->
Mitochondria anachloroplast
display

->
at least one of these cells engulfedaphotosynthetic prokaryote
ancestor of
I

Theory states -
an
early Eakaryotic becoming
chloro-
Cells ,
engulfed an
oxygen using nonphotosynthesis Plast

formed a relationship
Eventually the engulfed cell with the host

becoming endosymbiont
↳ of evelation ,
over the course merged
the host cell and its endosymbiont
into a single organism
 This
of Mitochondria
theory is consistentwith
many structural
features
and chloroplast

Mitochondria and chloroplast have two membranes

surrounding
them
↳
there's an evidence that the ancestral
engulfed Prokaryotes had two outer

membranes .

& Mitochondria and Chloroplast Contain ribosomes as well as

Circular DNA molecules .

# Mitochoderia and chloroplast are autonomus

somewhat independant
 ~ (cell Gas hundredne uter thousandest itever of Motabilic activity i
,

mitochoaria chemical
energy conversion
.

↓
found nearly all
it's in
eukaryotic cells
each of the two membranes that endoses the mitochondrion is a
collection of embeded
Phospholipid bilayer with a
unique

B
protieng .

"enhancing
[The outermembrane
↓
is smooth] productivity
i
the
,

give
folded into cristae] inneumitochonde
-

I innermembrane
membrane a
The innermembrane creats two compartments large surface
area
- -
enzymes
intermembrane mitochondrial A in matrix
space -narrow Matrix -catalyse

I
:

between and many steps of cellular

region inner contains
outer membrane different respiration
protiens that enzymes as well
makes ATP are ,
as mitochoderial
built in inner DNA and Ribosome
membrane
 -
↳

mitochodoria moves around its shape and

change
fuse or devide into separate
,

fragment
E
form tubular network that state
a
of flux mug in skeletal muscle
is in a
dynamic
this network has been

refered to as power gride"

 chlorplast capture of light
:

Scontains thegreen pigment to

chlorphyll enzymes
,
and other products that
function in the photosyntheticProduction of
sugar
.

3-6Mm in
length ,
found in leaves and other green organsof plants/algue

Contents of Chloroplast are partioned from the cytosol

by an envelope consisting of two membranes seprated by a
very narrow intermembrane space

-inside the chloroplast another membranous

system in the form of flattened interconnected sacs called

! stacked
thylakoids Thylakoid
&

into granum-
-
-

C stroma fluid outside the thylakoid

:
Contains Chloroplast DNA ribosome
as well
,

many enzymes
as
,
The membranes of chloroplast devide the Chloroplast
space into three compartments
↓
- stroma
-
intermembrane thylakoid
space space
* This compartmental organization enabels the chloroplast
to convert
light energy to chemical
energy A
Note
both chloroplast and
Mitochonderia are
mobile , move
along
track of cytoplasm

chloroplast are specialized memberof a

family of closely
related plant organelles called [Plastids3]
↳
- I
roots chromoplast
last ↳ has pigments that
[anylop
tubes

colorless organelle that gives fruits

and flows
their orange andyellow
his
stores Startch Samylose)
 Peroxisome oxidation :

C specialized metabolic compartment bounded by a membrane

H
peroxisomes Contains enzymes that remove hydrogen and
transfor them to
oxygen , producing hydrogen peroxide
L
some peroxisomes peroxisomes in

use
oxygen to break liver detoxify
down alcohol
fatty acids by
into smaller molecules
transfering hydrogen
that are
mitochondria
transfered to I
and used as fuel
from poisinous compounds to oxygen
 The HaO2 Produced peroxisomes is Poisonous itself
by
but the organelle also contains an enzyme that converts it to

I
water I reductase]

that Icroauce H2O2 and those who

Enzy mes

dispose of it
J
are sequestered away from other cellular
organnels that could be damaged

glyoxysome -> found in fat

storing tissues
of plants seeks
I
it has the fatty
enzymes that initiate conversion of
acides into
sug ars
-

peroxisomes grow large

made in
by incoporating protiens
cytosol and ER , as well
as lipids
made in ER and the proxisome itself
 figure's , J, !
L

5 = 51
Concept 7 6 - cytosheleton
-
- 3,31 91
↑

: ) - - S

Cytoskeleton network of fibers

extending throughout the cytoplasm
The most obvious function of
*
cytosheleton - .
mechanical support
maintain its
shape
·

cytoskeleton stablized balance between opposite forces

is
by a

exerted by its elements

cytoskeleton
location
dynamic , can be reassembled in a new

the
, changing shape of cell

cell
motility requires interaction o
cyto skeleton with
motorprotiens
5heletal elements works with plasma membrane
molecules to allow cells to move
along fibers outside
and inside the cell
↓

& visceles
containing neurotransmitters molecules
migrate to the tip of axons , the
long extensions of nerve

cells that release these molecules as chemical

signals to adjacent nerve

cells
minipulate plasmamembranes , bending
-

& cytoskeleton may

also
it inward from food vesides
 components of cytoskeleton -
↳ Microtubules
I intermediate fillaments
microfil laments
Omicrotubuls - hollowrods , constructed from globular
protien called tubulins-
=

each tubulin protien is air consistof two

slightly
lifferent polypeptides
u
I
& -tubulin ③ tubulin
* the two ends of Microtubule can differ
is one end can accumulate or release tubulin timers at a muc higherrate
thantheother -> This is called plus end
: microtubules
vesicles from ER to golgi
guidues apparatus
and from golgi to plasma membrane .

plant cells
I a ch centrosome
* in animal cells microtubuls grow out of we ↑ some

-
within the centrosome pair a
-
-
of
les

it is composed of nine sets of tripletsMicrotubules

 Cellular extensions that Contain
Cillia and Flagella ->

microtubules 9

propelled through water by

Many unicellular protists
act as
are

locomotor appandges
Cillia or flagella
* A each motile
⑧ cilluim
-
or flagella
I =>

Nine doublets of microtubuls are

arranged
aring of
in with two
in
aring single
microtubuls
-> 9 + 2"
arrangment
*** non⑧
motile
primary Cillia have a la to" patteren
to centricles
-Basal body my very similar
0

"to"arrangment
eN
the
9
basal
·
body of sperm enters the egg and become
entricles

&
dyneins :
Bending of cellia and Flagellum involves this
-

Motor protien
② microfilaments "actin fillament"
-

globular protien
a microfilament is twisted into a double chain of actin subunits

Is Cresent in all
Eukaryotic cells
three dimensional network formed microfilaments
*a
by
just to the inside of plasma membrane (cortical
microfilament) help support the cell's shape
I
This network gives the outer cytoplasmic layer of
a cell
[corfex] asemisolid
consistency
Bundels of microfillaments make up the core ot
Micro Villi
nutrient cells
~ in
absorbing
cause contraction of muscle cells
myosin
* in unicellular protist Amobea and some of our Whiteb,a
localized contraction and
amoeboid
by activ
myosin are brought by
Pseudopodia
-

↳ by extending a cellular extensions called

inplant cells activ protien confirbute to mic streaming is circular flow

of cytoplasm within cells

③ intermediate fillament -> animal cells

A even if the cell dies , intermediate fillment work often
Presist
* dead out layerof ourshin fullat-neratin fillaments
C -
anchoring of nuclear lamina
nucleas
 components of cytoskeleton

·
Microtubles (Tublinpolymer)
· Hollow tubes
· 25 n with 15nm lumen compression
resisting
·

·
Tubulin -> tubulin tubulin
maintance of cell ⑪ cell
③
~ motility
I
chromosom
⑭
mouments in cell division , organelle mouments

Microfilaments (Actin filament)

globular
·

·
Two intertwined strands of actin activ
monommen
·
Fam -
·
Actin tension
bearing elements
·
maintance of cell shaper, changes in cell shapes , muscle contraction

cytoplasmic streaming plants) , cell devision

intermediate fillaments
· fibrous Protiens Coiled into cabels
several different protiens
8-12 nM
·
·

(kerating
·
Maintance of cell shape tension bearing elements, anchorage of nucleus
and certain other organelles , formation of nuclear lamina
motor
Pro tien
attatches - -

to areceptor Two esicles

can "walk" Love a

tw
e
the vesicle
axon
a microtubul
along
-

->
-
or microfilament
-

--
 -
micro-tubuls
where
are initiated

↳ made up of
nontubulin
hat ↓ Sets of microtubuls
protien
connectimicrotubuls &
triplets

== C
 2 .
5
flagella
unmar
spen
cell udulates
snake like
motion driving in the the axis of flagellum
direction as
age
during
slowing - fresh
-
recovers water
strone it
,
Sweeps side
stroke
40-60 C

strokes X wass
a back
- - cillia have
and forth motion directin
moves the cellin
a
- perpendicular
to axis
of cikme

an aftatchet
called
have
- motor protiens
nein
P dy
-
-

C
*
↑

Sob
C

Entire
-

C
microtubul
The outer are
de gatherby
-

-
- 0 -
central
↓
-

- nine outer
connected
-
microtubul
two
- - -
doublet of nor
-

Cilluir extend by
-

-
-

rubulin
19 to
into basal I

doublet Body protiens arrangment

each another
joiicrotubuls two central
micurtubul
of triplets are not prest
to form a vin nine
 increase surface0
a

cellular e
reinforced by
bundels of
↳
tensions
mitmenttermediate
anchorament"
interactionof at e

myosinnt -

0
alayerof cy toplage cycles
the cell moving over
O
tracks of altir fillaments 0
motor drivestremi
Myosin with actin
by interacter -

I ↓
actinfillamen
eac myosinprojectionmy osizand
the parallel
drives

approach E
-

others Contra actinfillament Paste

Concept 7 7
.
extracellular components and connections
between cells helps coordinates cellular activity

strnir lature of plant cells

· maintain its shapeprotect the cell prevent
, ,

excessive uptake of water

·

prokaryotes , some protists and fungi also have cell

Walls
*
plant cell walls are much thicker than the plas ma membrane
A the exact chemical composition of the wall varies from species
to species and even from one cell
type to another

basic mesign of walls is consistent with

(nicrofibrils Addeofaccarat a a

protiens

synthesized by an
called
enzyme
cellulose
synthase
v

Primary cell wall :

-young plant cells Secrete

a relativly thin and flexible wall .

middle lamila thin between I

layer
:

crimary walls of
-

adjacent cells rich in

sticky polysaccharide called
Pectin .

cell wall between plasma membrane and Primary

secondary
:

cell walls
example wood consists mainly of secondarywalls
 Extracellular Matrix (ECM) of Animal cells

↳ ingredients of FCM are glycoprotiens and

main
other
carbohydrate-containing molecules -

The most abundant protien of ECM is Collagen which

forms fibers outside the
strong
↓
The
woven
collagen fibers are
out of
embeded in a network
proteoglycans
↓
cells
secreted by cells
infact collagen
account for about 40%
of total Protien in
human body

small core protien and many

carbohydrates chains
 attatched to ECMby ECM
some cells are
glycoprotiene such as
Fibronectin
I
fibronectin and other ECM Protiens bond to
receptor protien called
ins
a

built into plasma membrane

<
-

they span
embrane and -

an
transmit signals
their cytoplasmicsidee ee between the ECM and
filmants cytoskeleton
[integ rate changes o curring]
Example/some deve loping outside th?
and inside
cells in el

specific pathways
embryo migrateorientation
along
by matching the of their microfilament
to the "grain of fiber in the extracellular
Matrix

A extracellular matrix can influence activity of genes

in the nucleans

* mechanical signalling may occur through Cytoskeletalchanges

that trigger chemical signals
core
 cell junctions is
Neicommunicate
ghboring cells often adhere, interact and

throug direct
physical contact
↓
it that the of wall
living would isolate
seems non cell

plants but plant cell walls are perforated with

Plasmodes mata : -
channels that connect cells

The plasma membrane of

·

adjacent cells line the channel

of each plasmades math and
thus are continous

·
Because the channels are
filled with cytosol , the cells
share the same chemical
environment ,
By joining
adjacent cells , plas modesmata
unify cells into one living
continuum

·
water Protiens
, , BNAc solutes
freely
.

can pass
light junctions Desmosomes and Cap junctions in animal cells

↳ all
,

three
types are
especially common in

epithelial tissues

*Fight junction) ->Amembrane of neighboring cells

are
very tightly pressed against each other
*
forming continous seals around the cells , a
barrier
that prevents leakage of extracellular fluid of
across a
layer
epithelial cells

* Desmosomes) "anchoring
junction"
fastening cells to
gather
into
strong sheets intermediate ,

fillaments made of sturdy Keratin

Protiens anchor des mosomes in

cytoplasm
* (gab Function) "communication"
provide cytoplasmic channels from heart
muscels
or erx Do ein ne breas animal embroys
·

↑
molecules may pass
↳these protiens creat pores through which
small
 Chapter 8 ,
cell membrane

8 1 cellular membranes
.
are fluid mosiacs of lipides and

protien

Lipid and Protien are the staple ingredient of membranes , although

carbohydrates are also important ⑤
I
* The most abundant lipids in most
selective
membranes are phospholipids **
permeability
↳ Phospholipide is amphiatic molecule ,
has both
an
meaning it
a
hydrophillic and a
hydrophobic region
*a phospholipid can exsist as a stable
boundary
between two aqueous compartments because the molecular
tails from water while
arrangment shelters the
hydrophobic ,

exposing the hydrophillic heads to water

A like membrane lipide ,
most membrane protiens are amphipathic
such protiens can reside in phospholipid bilayer with
their hydrophillic region protru ding

S
Thi molecular
Contact of
arrangment
of protien
Maximizes

with water
hydrophillic regions
and extracellularfluid
a

cytosol in
while
providing hydrophobic parts with non-

aqueous soultion .

fluid mosiac model the membrane of mosiac is a

fluid
mosicc of
of phospholipides
protien bobbing in a
bilayer
ne a
- E
The protiens are not randomly
distributed in membrane, group
of protiens are often associated
functions
in long lasting
common
-me researches have also
found 9secific lipid in these
patches ->
lipid rafts
 The
molecules
fluidity
.
of membrane -> membranes are
-
- -
-
not
-
static sheets of

Amembrane to gather by
drophobithe
is held
e
weak interactions
e
scauses
fluidity hydrophobic core
· Most lipids and someprotiens can shift
sideways
-
Interal
or
very rarelys flip flop

The
sideway moument of phospholipas
:

-
is
Ed adjacent cells switch
·

about lot times persecond

positions

.
Protiens are much larger than phospholipides and move more
Slowly many membrane protien are held immobile by theirattatchment
E
to
cytoskeleton orextracellular matrix
some membrane protien tend to move in a highly
fibers by
directed manner driven along cytoskeletal
,
motor protiens ~
 -

- -

labeled differently indicates

at least one
↑
i I Plasma membrane
move sideways

&

A membrane remains fluid as temprature decreases

until the phospholipid e settle into
closely packed arrangement
a

and the membrane solidifies .

* * The temprature at which membrane solidify

depends of lipids
on
type **

temprature decreases
Sthe membrane remains fluid to a low temprature fails A*
if its rich in phospholipides with unsaturated hydrocarbon
Es unsaturated tails cannot pack to gather
The steroid cholestrol has different effects
, on membrane fluidity
↓ ↳
37%, human body lower temp reture
high tempretures
↓
make the membrane C
prevent i n g lightpacks
less fluid
by restraining high molecular
Phospholipid weight)
es - Cholestrol can be though of as
a
"fluidity buffer"
I

A compared to animals plants have low

verysteriod
levels of Cholestrol ; rather related
lipid buffer fluidity in plant cells
Evolution of differences in Membrane lipit compositions
Variation in the cell membrane composition of many species appears to
b
evolutionary adaptations that maintain the appropriate membrane
fluidity under specific environmental conditions

S
examcleofishes that live under extreme

I cold have membranes with

unsaturated
hydrocarbon tails
& Some bacteria and archaea
high proportions

thrive
of

!
at tempratures
greater than 90°c inthermal hot springs
and
geysers
Their membrane have unsual membrane lipide that
prevent fluidity
excessive of membranes at such
high
* The
abilityresponse
membranes
to
change composition of cell tempratures
its temprature has
evolved in
is in
changinglive where
that
organisms tempratures vary
③
many plants
that tolerate extreme colds Such
as winter-wheat the ,
percentage of unsaturated
Phospholipid increase autmn in , that keeps

membranes from solidifying in winter

 Fiberof extra
cellularmatrix glycolipids

peripheral -> Microfilamentat

* *
Protions
steriods cytoskeleton

Membrane protiens andtheir function

↳ More than 50 kind of protiens have been found in redblock
Cell Membranes

phospholipides form the mainfabric

of the membrane , but protiens
determines membrane's functions
 integral protiens Icentrate the
hydrophobic
:
· -

Emet
interiorof the lipid bilayer
transmembrane -
Majority are pan
the ane

interior
PThe region Consist of one ormore
Stretches of nonpolar amino acides
Typically
-

20-30
t hydrophillic parts of the Coiled into
molecules are to
exposed aqueous ↓helix
Solutions on either side of membrane Some Protiens
.

have one ormore hydrophillic channels that allows

passages of hydrophillic solutions to pass .

:
Peripheral Protiens :
not embedded in lipid
surface of membranes
bilayer
at all ; bound to the
loosely
often to exposed parts of integral protiens

Eraserresi
* -

C
Cytopl a smi c sidet
heldinplace by attatchment
to cytoskeleton e
forexample// in animal cells -> membrane protiens are
attached to fibers of extracellular Matrix
called integrine .

u -

1
-> bacteriorhodopsin
-

-
-

-
secondary
true e
C
↳
ne N tirminus outside C terminus
inside
*
non-heal
-

are in contant
with the aqueous solution in extracellular

and side
cytoplasmic
 ->
change
shape

a
hydri
protiens in a cell surface are important in the
medical feild as well ,

a protien called CD4 On the surface of immune cells

help the human (HIV) infect these cells
immunodeficiency virus
↓
resistant people have
that codes for
an
unusually form of agene
an immune surface protien
called (CR5

CDY is the main HIV receptor HIV must also bind to

, a CCRE as

a "Co-receptor ~ anabsence of CR5 prevents

the virus from entering the cell
Shey fortreatment of HIV infection - i n terferi
Side effects
n g with

↳
CDn causes
dangerous
dis covery of CCR5 provided a Safer
target for developments of drugs thatmash
this protien
 The Role of membrane
carbohydrates
in cell-cell
recog
nition

example/asorting ability
of cells into tissues , to

organs in an animal embryo distinguish

and one

type of neighboring
② rejection of foreign cels by the cell from another
immune system

cell other cells , often

to molecules
recognize by binding containing
Scarbohydrates on the extracellular surface of plasma membrane

Membrane
carbohydrates
usually mort arched
chains of fewer than I5 sug ar units
,

K ↳
bondedto
covelantly
lipids
covelantly
->
glycolipides S
bonded to protiens

glycoprotions
A The carbohydrates on extracellular silve of plasm membrane can

"vary from species to species A

The diversity of the molecule and their location enables
as markers from cell to
membrane carbohydrates to function one
the
variation in

another ·

Human A BABO blood types = carbohydrates part of

glycoprotiens
 Synthesis
and sidedness of membranes
The two lipids
may differ in lipid Composition and
layers each protiem
has directional orientation .

aysmmetrical of protiens
The
arrangment , lipide ,
and
carbohydrates as membraneis being built
-&
c -

D
-

O
C -
-
-

E
-
-

. . . . . .

E -

Oc
ept
8 2 .

membrane structure result in selective

permeability
selective
permeability -> allows substances to cross are
than Others .
easily

theabilityto
regulate transportacros
* learn
 traffic
a
steady
membrane in both
of small

directions
molecules and ions movee across the plasma

, other nutrients enter the cell and metabolic waste

acides
sugars , amino

leaves it - takes On for cellular respiration and expels co2

regulate concentration of in
organic ions ht ,
d ,
cat , at

do not
↳ substance cross in
discriminately
The permeability of lipid
Bilayer
The Non-polar molecules , such as
hydrocarbon , con , on are

hydrophobical lipides They

are

without the aid of

. can all dissolve
protiens
in lipide bilayer
easily , membrane .

Polar molecules
, ions cannot
directly pass
I even water
,
avery small polar molecule does not
cross rapidly relative to non-polarmolecules .

a
charged atom or molecule and its surrounding of
shell water
interior of protiene
, are even less
likely to penterate the hydrophobic
Transport Protiens
I transport
specific ions and

Protien
variety
:
of polar molecules cannot

-"Channel Protient
-

-
,
move through cell membrane units own
hydrophillic channel
that certain molecules
or ions use as a tunnel

↳ for example passages of water

,
known as aquaporins
is
greatly facilitated
by channel protiens
↓

consists of four identical

·

polypeptide subunit ,

· each
water
polypeptide creats a channel that
Pass
·
it allows overall entries of 3-billion water
molecule /Te second
②"Carrier protien" hold on otheir
- passangers
and its to shuttle them across the membrane
chang shape in
away
a transport protien specific for the substance it
certion substance a
translocates(oves allowing only
, a

for example/glucose carrie protien in plasma membrane

of red blood cells can
transport glucose 50 , rou faster
than glucose can Pass on its own
- its so selective it even rejects
fructose
 ↑

Concept 8 3 ->
.

Passive transport is diffusion of a substance across

a membrane with invesment

no
energy
diffusion movment of particles of any substance so they spread out

b ammic
-
:

into available space

equilibrium will exist

from high concentration to low concentration - it diffuses

down its concentration
gradient->unae enteres
-

example/uptake of
oxygen by
a cellular respiration

oxygen diffuses into cells across Plasma membran , as

long
as cellular respiration consumes the Or ,
diffusion into cells will continue

* diffusion of substance across a biological membrane is

called passive transport because it
requires no energy * A
 Effects of Osmosis on water balance

membranes are foo small for sugar molecules to pass, but

large enough for water molecules
. However, light clustering
of water molecules around
hydrophillic
solutes makes
some of the water unavailable to cross membrane

! solute with high solute concentration has a lower free

-

water concentration .

I water diffuses across the membrane from

regions with
high free concentration (lower solute contration) to that
of lower free water concentration (high solute concentration

OSMOSiS : -

diffusion of free water across a

selectivity permeable membrane

 Tonicity
cell to
->
or lose
The
ability
water
of
Surrounding solution to cause a

I ain
↳ depends on
parts of concentration of solutes that cannot cross

cell membrane

in a cell without a cell wall , such as animal cells

the cell will be immersed environment that
in an is
stone
,
There willnot be

hypertonic
the cell
:
-

non
will
pentrating solutes
lose water shrivel and
no net movment

die
,
probably
, if a lake becomes
hypetonicand(increase level of

die
salinity
an animal might shrivel
hypotonithec -> water will enter
cell will swell
cell faster than it leaves and
and
lyse(burst)

water balance of Cells with cell walls

↳ the cell wall help maintain the cell's water balance

the plant cell walls Swells it enters

as
by osmosis, However

relativy inelastic cell wall will expand so much before it exerts force back

on wall ->
called Sturgor) Pressure

Turgid healthy state for most plant cells

& plants that

-

arenot woody depends for mechanical

support on cells kept furgid

flaccid > There's no tendency for water to enter

cellwate
Plasmolysis Plant see shrivel ,plasma membrane pulls
away
front multiple
places
need
diffusion : -

Passive transport by the aid cl protien

I
many polar molecules are blocked by lipid bilayer ,

they
diffuse
helpof transport protiens
passively with the

Most transport Protiens are

very specific thing transport
substances but not others

- -
carrier channel

allow molecules to diffuse

from one side
very
quickly
of membrane to another

A
aquaporins -> Facilitate the massive levels of

I
diffusion of water that occurs in plant or animal
cells
of aquaporins
ex/certain Kidney cells have a high number
allowing them foredain water from urine before its excerted
 Channel Protiens that transportions are called ion channels

function channels which opens or

as
gated close in response to

electrical stimulus abows astream of

Potasuim to leave the
Chemical Stimulus cell

⑤ when a substance binde to channels

carrier protiens such as transporter seems to

*
glucose
undergo a subtle
changein shape that somehow translocates
the
solute-binding site across membrane
AA

concept 84 Active transport to move

energy
uses
. :

solutes their
against gradiant
Active transport transport that moves solutes
against
their concentration gradiant
all carrier protiens rather than channel protiens
E
 Active transport enabels a cell to maintain internal concentration

of small solutes that differ in concentration in its environment .

animal cell has a much

* an
higher Concentration of
Potassuim ions (k) and much lower of Soduinions at

as in other
types of cellular work ATP
hydrolysis
:
supplies
the
energy
for most active
hydrolysis
its terminal phosphate group is transferred
to the transport Protien [can induce protients
directly
change
its shape]
Sodaim Potassium Pump -

exchanges Nat ,
At across Plasma membrane
of cels
① cytoplasmic Nat binds to soduin-pottasium pump with high affinity when
the protien has this shape

⑳
Binding of Nations Simulates-
phosphorylation by a kinase
using at
③phosphorelation leade to a change in protien' shape reducing its affintyfat ,

Navelen 3
has affinity for ki 24" bind the extracecular
sike
on
triggering release
⑰ new shape
, ,
, a
⑥24t realesed are
of Proe

⑤ loss of Phosphate group restores protien's original shape, lower affinity for let affinity
again ,
for Nat is high
cycle repeats
or carrie
How IOR Pumps Maintain membrane Potential
side of
cytoplasmic membrane is
negative in
charge relative to the extracellular

due to unequal distirbution of anions and cations on the two sides

membrane Potential : -- 50 to -200 millivoltes

↳ affects the traffic of all charged substances

The membrane Favors the Passive transportof

cations into the cens and anious outside the cent
chemical force
Firm concentration
gradiat
electrochemical
gradianet Le
Combination
membrane
Potential
electrical force
anion diffuses not simply down its concentration gradianet
but its electro chemical gradient
- en
opposite direction
if electrical and ↓
chemical contirbutions active transport
directin
in thesame electrochemical
:
may be nessacey
gradient
 some protiens that
activly transportions contirbute to membrane
Potential

electrogenic Pump
atransport that examples

genrate voltage Ganimal Potassuin

!
:
-
-

across a membrane
↳odum Pum

I
plant fungi bacteria
, ,

helps store energy

Hydrogen Dump
that can be trapped
forcellular work
-
ex use of a during cellular
respiration
 Cotransport :

coupled transport by amembrane protien

a solute that exsist in different concentrations across a membrane can do work

as it moves across that membrane down its concentration gradient

Cotransport : atransport Protien CCo transporter) can couple the down will diffusion
of the solute to the "uphill" transport of protiena
against its concentration gradient
↓
plant cells uses the
gradiant of H generated by its ATP-powered
Proton pumps to drive the active transport of amino acids several other
,
sugars ,

nutrients into the cell .

-> active
transport

dince
Fration
gradient
a Co-transporter couples the
C
return of Ht into the cell
to transport of sucrose into the ceee its concentration gradient
against
 TheH protien uses the transport Protien as an avenue to diffuse down

E Plants
its electrochemical gradianet , which is maintained by proton pump

use HY sucrose Cotransport to load Sucrose produced

by photosynthesis into cells the vein of leaves The vascular
.

in

tissue of the plant cell then distribute to roof and other

non-photosynthetic that do not make their own

organs sugar
.

eAnimal transports Nat into intestinal cells to

gather
With
glucose
E Nat then pumped out of
moving,its which is concentration gradient
is the the cell into blood on the other
Side
by Nat/k+ Pumps

Eq
↓
⑧
Natylucosefindtransporters has
co

helped us more effective E

for when
treatment
Normally Soduim waste reabsorbed in the Colon
,
is
maintaining
Constant levels , but diarrhea expels waste rapidly so

E that reabsorption
in the
body and Sodanim levels fall
is not possible
precipitously
treat this life condition ins
To threathing
Concept 85 Bulk transport across the plasma membrane occurs by exacytoic
.

and
Endocytosis
A
large molecules , protiens and polysaccharit
such as

generally don't cross the membrane by diffusion transport Protien or

but instead
"packaged vesicles in

Exocytosis -> The cell secretes Certain molecules

Fusion of vesicle with the plasm membrane
by

A transport vesicle that budded from golgy apparatue

! moves
* when
along microtubule of
vesicle membrane
cytoskeleton to the plasma membrane
and plasma membrane come into contact

specific protiens in both membranes

rearrange the lipid
molecules of two membranes fuse ; contents of
mean -

vesicles spill out of cell , the vesicle become

part of Plasma membrane
 C
I
Examples panceritic

I
cels
-

cells in Panceas that make insulin secrete it into extracellular

fluid
by exocytosis
A neurocells use exocytosis to release nuerotransmitters
that signals other nuevons or muscle cells

* when cells exocyto sis delivers Some

of the
are
makingandcell walls ,

necessary protiens carbohydrates from Golgivesicles to

outside of the cell

Endocytosis
6 The cells asin molecules and
-
pic
rate matter
by forming
new vesicles from Plasma membrane
A
although protiens involved are different endrcytosis looks like the reverself exocytosis
,

D Small area of plasma membrane sinks inward to form a

Pocket
② as the Pocket deepens it pinches in forming
, a veside

Containing material that has been outside the cell

* phagocytos is a cellular
a
engulfs
cell
eating a * pino
cytosis - cellular

particle by extending drinking

a cell
psuedopoduim
and
around
within
continually
drops of extra
galps
fluid
it
Package it cellular
into formed
a membranous sac called
tiny resides
un
food vacuole .

The particle infolding

byPlasma of
will bedigested afterfoodvacoule membrane

fuses with
lysosome containing in this
way
the cell

hydrolytic enzymes obtains molecules dissolved

indroplets any and all
;

solutes taken
by
pinocytosis are

many
in cases, plasma membranes < non specific for
that form vesicles are lined on their
cytoplasmic the substance it
Side by a
fuzzy layerof coated protiens called pits
transport
S resulting pits
s.

are called coated pits

& Receptor mediated enducytosis
E
specialized type of pinocytosis
that enabels to
cells
aquire balk
quantities of specific substances ,

everthough theyundeinter
specific solutes binds to receptors ,

The receptor protien cluster in

Coatedepits and forms a vesicle
containing the bound molecules .

After the material

ingested is librated
from the vesicle ,
the empited receptors are
recycled .

& C -

Cholestrol travels in blood

in particles called low
density
lipoprotiens (DLs) , CDLs bind
to LDL receptors on Plasma membrane
then enter cells endocytosis
 level of cholestro it
Hyperchesternia -
very high
I
IDC cannot enter the cell because (DL
receptors defective
are
or
missing
cholestrol accumulate in blood
atherosclerosis causing
early ↓
This the space in vessels
narrows
and impede blood flow causing heart attack
and stroke .