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Unit 2 Molecular Biology
Biology SL
IB
High School - US
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2 Molecular
Biology
the
study
of the structure
and functions of
molecules that are
essential to life
Molecular
biology
:
living
processes
interms ofthe
chemical
substances
involved
explains
living
processes
intermso&thechemical substancesinvolved
the
study
ORthe structure andfunction of molecules
thatareessential
to life
organic
Molecules are
large
compounds
synthesized
by
living
organisms
'
carbon-bas#
Stablecompound
→ carbon compounds
can
form four covalent bonds ,
allowing
a
diversity
of
sseble compounds
to
exist
this is because
oftheir
valenceelectronstructore
There are
four
primary
types
or monomercarbon compounds
that make
up
materials
in .
livingorganisms
Amino
Acids
Fatty
Acids
Carbohydrates
Nitrogenous
Bases
'
N
t
/
glycerol
monosaccharides
→
nucleotides
1.
t
i t
Poly
- DNA /RNA
proteins phospholipids
saccharides
Urea
:
organic
compounds produced
by organisms
when
they
breakdown
proteins
0
→
excreted
from the
body
through
urine
I
→
organic
but can
be
synthesized artificially
c
l
t
HZN
NHZ
first
time this
occurred
→ helpedfalsify
vitalism but
did not disprove
molecules are
constantly being
synthesized
and
broken down via
enzymes
Metabolism:
the wets of all
enzyme
catalyzed
reactions in
a cell/
organism
Two
pathways
-
Catabolic
nullAnabolic
→
thebreakdown
of
complex molecules
into
→
the
synthesis
of
complex
molecules
simple
molecules
including
from
simpler
molecules
including
the
hydrolysis
of macro-
the
formation or
macromolecules
molecules into
monomers
to monomers
by
condensation
→uses
hydro
/ isis
( addition
of
reactions
water
)
→
polymers
are brokendown
by
→
remove water
between
adding
H2O
and
breaking
monomers to
form a new
covalent bonds
covalent
bond
→
builds
up
polymer
chains
→ Examples:
food
digestion
cell
respiration
protein
synthesis
in ribosomes
- DNA
synthesis
photosynthesis
""
"
'""med
.my,
,,
,,
→
"
""
÷÷F÷:÷:÷÷÷.
.
was
, remove
,
|
.wager added
|
.Éy→M
molecule
:
atoms
bonded
by
covalent bond
Urea
organic
compound
thatis
produced
by organisms
when
they
break
down
proteins
→
excreted from
the
body
through
urine
→ can
be
artificially
synthesized
ina
laboratory
synthesis
of
Urea
0
→
nitrogen
containing
compound
component of
urine
I
→
catalyzedby enzymes
in
the liver
t
→
transported
to
kidneys
to make wine
HZN
NHZ
→ 100 mil . tonnes
produced ,
used as
nitrogen
fertilizer
Vitalism
:
theory
that the
origin
and
phenomena
of life
are due toa
vital
principle,
which is different
from
chemical or
physical
forces
→
organic
compounds
could
only
be made withthe
help of
a vital
principle
the artificial
synthesis
of urea
helped falsify
vitalism
accepted
that
processes
in
living
organisms
are
governed
by
same chemical and
physical
forces as in non
living
matter
- 2 Water
Hydrogen
bonding
in water
water molecules are
polar
and
hydrogen
bonds
form
betweenthem
by
covalentbonds between 1
oxygen
and 2
hydrogen
involves
unequal sharingof
electrons
→
polar
covalent bond
(
oxygen
nucleus
moreattractive
)
oxygen
has
partial
negative charge
,
hydrogen
is
partially
positive
- the attraction
between water molecules is
a
'
hydrogen
bond
'
11mF
)
Cohesive
Properties
hydrogen
É
bonds
④
binding
of
two
watermolecules
/
.
'
'
hydrogen
④
⑤
.
-.
due
to
hydrogen
bonding
|④
:
Useful for
water
transport
in
plants
.
.
hydrogen
covalent
⑤
oxygen
bond
Adhesive
Properties
covalent
forming
hydrogen
bonds between waterandother
polar
molecules
useful
in leaveswherewateradheresto cellulosein cell walls
thermal
Properties
high
specific
heat
capacity
:
large
amounts
of temperature(
energy
changes
cause
hydrogen
bond
breakage
or
formation
.
water
temp
is
relatively
stable compared
toair
and land
thermally
stable habitat
for aquatic organisms
high
latentheat of
vaporization
: heat needed to
formvapour
molecules
good
evaporative
coolant
(
ex
:
sweating
)
high boiling
point
:
highest
temp
reachable ina
liquid
state
broad temp
range
10
-100°C
)
found
in most habitats
on
earth
Carbohydrates
t
Lipids
carbohydrates
monosaccharide monomers
linked
together by
condensation reactions
to
form
di
- and
polysaccharides
°
mono :
single sugar
units
(
ex
:
glucose
, fructose
and
ribose
)
°
di: two
monosaccharides linked
together
(
ex: sucrose )
.
poly
:
many
monosaccharides
linked
together
(ex
: starch ,
glycogen
,
cellulose
)
- Combine
through
a condensation reaction
→ loss
of
an
OH
from
one molecule
→
loss of
an
H
from
another molecule
"
linking
monosaccharides
is an anabolic
process
t
requires
energy
todo it
Lipids
a
diverse
group
of carbon compounds that are all insoluble in water
Energy storage
lipids
aremore
suitable
for
long
term
energy
storage
in humans ,
than in
carbohydrates
→
theamount
of
energy
released
from lipids
during
cell
respiration
is
double that
of carbohydrates
(
ableto storemore
energy
at the
same weight
→
good
heat insulators (storedin
fat
in our
body
)
→ acts
as ashock absorber (stored
around internal
organs
)
Body
Mass Index
Bmi
Tn7igihn
.
BY/usnYIw-um
.
- normal
overweight
730 Obese
Fatty
Acids
:
building
blocks
of lipids
. Unsaturated
fatty
acids have
double
covalent
bonds
f \
double bonds causes
Kinks in the
shape
unsaturated
. mono saturated
only
one
double bond
affronted
ldwbnkonds
)
poly
saturated:
"
multiple
double bonds
double
bonds
)
Saturated
fatty
acids
have
the
maximum
number of
C- H
bonds
only
have
single
- covalent
bonds
relatively
linear
the double bonds of U.
fatty
acids
affect
their
overall
shape
( is
fatty
acids
have H's on
the same side
of
the
double
bond
H
H
H
O l l l
c
C
c
=
c
H
f
bends the
O
I
\
molecule
/ C
H
H s
A
Trans
fatty
acids have His on
opposite
sides
H H H
Ox
l l l
o
e
- c-
c=c
c ←
Fifer:stays
H
'
l l
l
H
H
H
Triglyceride
molecules are the main
components of
fats and oils
→
formed
through
condensation
of
3
fatty
acids t
glycerol
H O
' "
H
C- O
C
cuz
... CH
z
C
Hz
\
o
H
c
O
"
c
cuz
..
.
cuz
cu
,
t 3h
####### I
%
H
C
O
C
Ctlz
..
. CH
z
- C
Hz
l
H
4 Proteins
polypeptides
are chains
of
amino
acids
formed
by
condensation
reactions
happens
on
ribosomes
during
translation
polypeptides
arethe main
component
, proteins
can have one
ormore
polypeptide
during
condensation
reaction
,
peptide
bond
is
formed
H
H
H
,
I
,
¥ 0
H
,
I
←
O
N
c
c t N
c
c
C
H
I
H
I
'
OH
R v
R
y
tho
/
L
H
H
H
l O O
- I
l
E
N
C
C
N
c
C
H
'
I
/
I
'
OH
R
peptide
R
bond
The R
group
of
anamino acid
specify
the
type
of
amino
acid it carries
creates
diversity
20
different
amino
acidsare usedin ribosomes to
unique
polypeptides
'
some
proteins
canbe
modified after
a
polypeptide
synthesization causing
further
changes
example
:
collagen
→
contains
proline
which makes itmorestable
Hypotheses
on
the
origin
of
amino
acids:
→ the
20 differentaminoacid were produced
via chemical reactionsbefore
life
was created
→
they
arethe ideal amino
acids
for
making
proteins
- natural selection
favors
organisms
that usethem
→
life
hasevolvedfrom
single
species
that used these
amino acids
difficult
to
add
orremoveones
from
the repertoire
Discrepancies
inthe
theory
:
→
some species
useoneof
3 codons that
normally
signal
theend
of
synthesis
toencode
for
anextra
amino
acid
Polypeptide
Diversity
ribosomes
canmake
peptide
bonds between
any
pair of
amino
acids
,
so
any
sequence
is
possible
→
all
possible sequences
for
amino
acids are
effectively
infinite
→
living
organisms
only
produce
a small number
of
these
sequences
the amino
acid
sequence
isstoredina
gene
in
coded
form
three bases
of
a
gene
code
for
anaminoacid
extra base
sequences
are
placed
at both ends and
occasionally
inthe middle
Some
proteins
are
single
polypeptides
while others
are twoor more
Examples
:
Integrin
- 2
,
unfold
t move
apart
when
working
Collagen
- 3
,
wound
together
toform
a rope
- likemolecule
,
allows
stretching toreducechance
Hemoglobin
4
,partsjoin
together
to
transport
oxygen
of
breaking
efficiently
Protein
conformation
= 3-D structure
determined
by
the amino
acid
sequence
a
protein
Fibrous
proteins
are
elongated
in a
repeating
structure
(
collagen
)
Globular proteins
have an intricate
shape
thatincludes
helical
parts
polypeptides
foldup
as
they
are made
→ stabilized
by
bonds between
R
groups
→R
groups
are
hydrophilic
if
they
dissolve
in
water
Examples of proteins
Rubisco:
most important
enzyme
→ the
shape
tchemical propertiesof
the active
site
allowit to
catalyse
the reaction
that fixes
CO
fromthe atmosphere
→
provides carbon compounds
needed
by
all
living
organisms
→ mostabundant protein
(presentin
leaves
)
Insulin
→ hormone
is
produced
asa
signal
to
many
cells inthe
body
to absorb
glucose
and help
reducethe
glucose
concentration
in theblood
→
shape
t chemical properties
correspond
tothe
binding
site
on the
receptor
→ secreted
in
the
pancreas
and
transported
by
the
blood
Immuno
globin
:
antibodies
→ havesitesat the tipsof
theirtwoarmsthat bind
to
antigens
→
they
act
as a markerto
phagocytes
→
binding
sites
are
hyper
variable
→
body
can produce
many
kinds
Spider
Silk
→ produced
by
spiders
→
dragline
silk is
stronger
than
steel
→ extensible
t resistant to
breaking
Proteome
all the
proteins produced by
an
organism
→
unique
toeach
person
due
to
different
aminoacid
sequences
fluorescentantibodies
to
identify if
a
protein
is
present
→ shows what is
actually
occurring
in an
organism
- 5
Enzymes
enzymes
are
proteins
that
speed
up
specific
chemicalreactions (anabolicorcatabolic
)
has an
active site
that allowsitto bind
toa
specific
substrate to
form
a
product
enzyme
product
substrate
→
'
enzyme catalysis
involves molecular motion
andthe collision
of
substrates
with the active site
- the
substrate molecule is
complementary
to the substrate molecule it binds to
. when the substrate
collides with the
enzymes
active site
,
they
form
the
enzyme
- substrate
complex
"
the
enzyme
remains
unchanged
and canthen bind
to
another
substrate
The
specificity
of
enzymes
is
often
called thelock
and
key
model
,
since
only
one
specific
substrate
can bind to eachactivesite
Enzyme
Rates
the
function
of
an
enzyme
isto increase therate
of
reactions
- rates canbe
affected
by
environment
including
:
→
temperature
→
pH
→
substrate concentration
enzymes
can
denature
when
exposed
to conditions that interfere
with
internal aminoacid interactions
when an
enzyme
denatures
:
→
the
bonds
including
IMF bonds
)
are
broken down
→theactive site
changes
t the substrate
willnot
fit
7
the
enzyme
does
not
die
each
enzyme
has
optimum
conditions
for
the
most
effective
reactions
- related to
cells location
inthe
body
→ 37°C
,
pH
7 in human
body
high
temps
cause
enzyme
to denature
,
causing
a decreasein
activity
low
temps
reduce the amount
of
molecularcollisions
,
causing
the reactionrateto fall
enzymes
denature
if pH
conditions
becometoo basic
or acidic
→
pHvaries
widelyamong
enzymes
Substrate Concentration
: the amount
of
substrate
availabletothe
enzymes
activesite
→
asconcentration increases
,
reaction rate increases
→
as concentration decreases ,
reaction rate decreases
when
all
enzyme
activesites
are
filled,
the reaction
is
saturatedt the
rate
plates
6
Structure
of
DNA
t
RNA
symbols
for
subunits
:
O
circles for phosphate
nullpentagons
for pentose
sugar
nullrectangles
for
bases
nucleotide
DNA structure
consists
of
:
→ each strand consists
of
a
chain
of
nucleotides linked
by
covalent bonds
→two parallel
strands
but in
opposite
directions
( f
3 ,
)
→ the two strands are wound
together
to
form
a double
helix
→ the strands are held
together byhydrogen
bonds between the
complementary
paired
nitrogenous
bases
DNA structure models
- Crick
t
Watson
discoveredthe DNA structure
by testing
&
building
models
first model
:
triple
helix
,
bases on outside
,
magnesium holding
the
two strands
together
→
rejected
when
Franklin
pointed
out that
not
enough
magnesium
. would be an
able
to linkthe strands
together
Watson tCrick realized thetwo strands mustbe
anti-
parallel
and theamount
of
A should
equal
T
and
Cshould
equal
G
built
second model
using
metal
rods t
clamps
and corrected
bond
lengths
tangles
→concludedto
be the correct structure and
suggested
a mechanism
for copying
DNA
&
genetic
code mustconsist
oftriplets of
bases
Helicase
the separation
of
the DNA strands is carriedout
by
helicases
→ a
group
of
enzymes
that
use
ATP
energy
to
break the
hydrogen
bonds
between bases
→ consists
of
6
globular
polypeptidesarranged
in
a
donut
shape
they
assemble withone strand
of
DNA
passing through
the center
of
the donut
and
helicase moves
along
theDNA strand
→
helicase
alsounwinds thehelixatthe same time it
separates
the strands
DNA
polymerase
each strandacts
asa
template for
the
formation of
a new strand
the
assembly
of
new
strands is
carried out
by
the
enzyme
DNA
polymerase
→
DNA
polymerase
moves
along
the
template
strand in
the same direction
,
adding
nucleotides
oneat
a
time
→
DNA
polymerase
brings
nucleotides intothe position where
hydrogen
bonds can
form
Once
hydrogen
bonds havebeen formed
between the
bases
of
the
two strands
,
DNA
polymerase
links
the
nucleotides
of
thenew
strand
together by attaching
the
phosphate group
to
pentose
sugar using
covalent bonds
→this
process
is
done with a
very
high
degree
of
fidelity
- fewmistakes
are
made
PCR
- the
polymerase
chain reaction
a
technique
used
to make
copies of
aselected DNA
sequence
→
only
a small
quantity
of
DNA
is
needed
DNA is
loaded
into a
PCRmachine in which
a
cycle
of steps
repeatedly
doublesthe
quantity
of
the selected DNA
→ DNAis heatedto a
high
temp
. so
the
hydrogen
bonds break and is cooled
to
form
hydrogen
bonds
The PCR machine heats to 95°C
for
15 Sec. to
separate
strands
,
then cools
quickly
to
54°C to
allow re
annealing
of
parentstrands
to
form
double
stranded .
DNA
There
is an excess
ofprimers
are
present,
which
kind
rapidly
to
target
sequences
,
which
prevents
the re
annealing
of
parent
strands
The next
stage
in
PCR is
synthesis
of
doublestrandedDNA
,
using
the
single
strands
with
primers
as
templates
Tag
DNA
polymerase
is
used in
this
process
:
→
enzyme
found
in hot
springs
→ has
a
high
optimum temperature
Tag
DNA
polymerase
works under
very
hotconditions and denaturesthe
DNA
template
to
separate
theDNA
strands
The
enzyme
thenadds 1000
nucleotides
per
min
(
a
very
rapid
rate
of
DNA
replication
)
which is
possible
under hot
conditions
→ a
cycle
of
PCR can
be
completed
inlessthan two minutes
Unit 2 Molecular Biology
Subject: Biology SL
IB
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