BAHAN KULIAH BIOKIMIA POWER POINT BAGIAN 1 /BIOCHEMISTRY POWER POINT LECTURES PART 1 | Karya Tulis Ilmiah
What distinguishes living organisms?
1. Structurally complicated and highly organized
a. intricate internal structures
b. many kinds of complicated molecules
proteins, DNA, RNA, starches, and lipids etc. (inanimate objects
sand clay are mixtures of simple compounds)
2) Living organisms:
a. extract
b. transform
c. store
d. use
ENERGY
1
3
Living things can extract energy from the environment
Chemical: Chemoautotrophs or lithoautotrophs
H2S 2H+ +S +2e2NH3 + 4O2 2HNO3 + 2H2O
4FeCO3 + O2 + 6H2O 4Fe(OH)3 + 4CO2
or
Sunlight: Photoautotrophs
nCO2 + nH2O (CH2O) + nO2
Energy is needed to build and maintain structures
a) mechanical energy
b) chemical energy
c) osmotic energy
d) light energy
- muscles
- electric eel
- plant turger
-bioluminescence
4
3) Most characteristic attribute of living things is selfreplication and self assembly
it is the quintessence of the living state
1 single bacteria 109 in 24 hr
inanimate matter does not do this
also the near-perfect fidelity of this process is awesome!
A crystal at equilibrium grows but life at equilibrium is
death!
Life is a set of relationships characterizing the nature, function and
interaction of biomolecules.
5
Philosophers thought life contained a “vital force” or
vitalism but this has been rejected by modern science.
Important insights and practical applications in medicine,
agriculture, nutrition and industry have come from
Biochemistry but ultimately biochemistry is still concerned
with the
WONDER OF LIFE
A Brief History of Biochemistry
6
Early 19th Century
World made of either "living matter" (organic) or "non-living
matter" (inorganic).(Vitalism)
1828 Friedrich Wohler accomplished the synthesis of Urea from
inorganic matter.
1897 Edvard and Hans Buchner showed dead cell extracts can
perform reactions of living cells.
The molecules responsible for performing these reactions
are called enzymes
Late 1800's Emil Fischer suggested key/lock picture.
Substrate Key, Enzyme Lock
Early 1900's Field of biochemistry emerges
Structure and function of enzymes
Elucidating enzymatic pathways
1944 Genes composed of DNA
1953 Watson and Crick determine the structure of DNA
Biological function linked to the information in genes
Double helix slide
Phylogenetic Tree of Showing Three domains of Organisms
How did organisms evolve?
• Blind watchmaker principle, small
mutations arise at random.
1. Evolution is not directed
2. Evolution requires in-built sloppiness
3. Evolution is constrained by the past
4. Evolution is ongoing
10
CAN you name a few of the recent discoveries?
Range of Life- Hot springs -subduction zones -artic
tundra- Antarctic dry fields - from animal intestines to
college dormitories. These are all equal to specific
biochemical adaptations.
Is Life Unique to Earth?
Tools of the trade
3D models space filling or stick models
H - white
C - black
N - blue
O- red
P - yellow
S - yellow
•Stick or skeletal models show molecular frame work
but not atomic radii
•I suggest that you get a model set to help with
steriochemistry and structure.
Physical Units of Space, Time, and Energy.16
LENGTH You must know this and be comfortable using them.
Length is very important!!
•C - C bond is 1.54 Å
•Hemoglobin 65Å
•Ribosomes 300Å
•Viruses 100 - 1000Å
•Cells 7 m or 7 x 104 Å
1Å
10-10 m
10 Å
10-9 m
100 Å
10-8 m
1 mm = 10-3 m
1 m = 10-6 m
1 nm = 10-9 m
1000 Å
10-7 m
104 Å
10-6 m
105 Å
10-5 m
Limit of a light microscope = 2000 Å or 0.2m
1 Å 104 Å knowledge comes from X-ray crystallography, electron
microscope or atomic force microscope
Life is in constant flux
17
Enzyme catalyzed reactions- Substrates Products 10-3 sec - milli sec
Unwinding of DNA 10-6 sec - micro sec
10-15 s
femto
10-12 s
pico
•femto fs
•pico ps
•nano ns
•10-8 10 ns
•micro s
•milli ms
•103
•2.3 x 109 sec
10-9 s
nano
10-8 s
10-6 s 10-3 s 10 s 103s
micro milli sec
excitation of chlorophyll
charge separation in photosynthesis
hinge protein action
fluorescence lifetime
DNA unwind
enzymatic reactions
generation of bacteria
average human life span
Energy
Ultimate source of energy is the sun
E = h 57 Kcal/mol of photons green light
or
238 KJ/mol
1 cal = 4.184 joules
0.239 cal = 1 J
You must know how to convert between the two.
ATP energy carrier, for hydrolysis to ADP + Pi
= 7.3 kcal/mole or 30.5 KJ/mol
While vibrational energy infrared) = 0.6 kcal/mol or 2.5 KJ/mol
C - C bond = 83 Kcal/mol or 346 KJ/mol
the framework of a carbon skeleton is thermally stable
but
non-covalent bonds are only a few kcal/mol or
10-20 KJ/mole
18
19
Thermal
Noncovalent
1
ATP Green
bond
light
10
100
C-C glucose
bond
1000
Kcal/mol
KJ/mol
1
10
100
1000
Biomolecule shapes and interactions are mediated by 4 types
of non-covalent bonds.
These bonds are responsible for the overall shape and interaction among
biomolecules and can be modified by thermal energy.
Boil an egg, fry a steak or get a sunburn.
1)
Electrostatic interactions
by coulombs law F= kq1q2
r 2D
20
q are charges
r is radius
D = dielectric of the media, a shielding of charge.
And k =8.99 x109Jm/C2
D = 1 in a vacuum
D = 2-3 in grease
D = 80 in water
Responsible for ionic bonds, salt linkages or ion
pairs, optimal electrostatic attraction is 2.8Å
2)
Hydrogen bonds
O-H N
2.88 Å
N-H
O
3.04 Å
H bond donor or an H bond acceptor
N H
O C
3-7 kcal/mol or 12-28 kJ/mol
very strong angle dependence
21
.
3)
22
van der Waals attraction
Non-specific attractions 3-4 Å in distance (dipole-dipole attractions)
Contact Distance
H
C
N
O
S
P
Å
1.2
2.0
1.5
1.4
1.85
1.9
1.0 kcal/mol
4.1 kJ/mol
weak interactions
important when many atoms
come in contact
Can only happen if shapes of molecules match
Steric complementarity
23
•Occurs when large numbers of atoms are in contact
Specificity
When there is a large affinity for a unique molecule to bind to another
a) antibodies
b) enzyme substrate
c) restriction enzymes
Dielectric effect
hexane
benzene
diethyl ether
CHCl3
acetone
Ethanol
methanol
H2O
HCN
D
1.9
2.3
4.3
5.1
21.4
24
33
80
116
24
H2O is an excellent solvent and dissolves a large array of
polar molecules.
However, it also weakens ionic and hydrogen bonds
Therefore, biological systems sometimes exclude H2O to
form maximal strength bonds!!
4*
Hydrophobic interactions
25
Non-polar groups cluster together
G = H - TS
The most important parameter for determining a biomolecule’s shape.
.
Entropy order-disorder. Nature prefers to maximize entropy “maximum
disorder”.
How can structures form if they are unstable?
Are they unstable? Structures are driven by the nature
of water interactions
1. Structurally complicated and highly organized
a. intricate internal structures
b. many kinds of complicated molecules
proteins, DNA, RNA, starches, and lipids etc. (inanimate objects
sand clay are mixtures of simple compounds)
2) Living organisms:
a. extract
b. transform
c. store
d. use
ENERGY
1
3
Living things can extract energy from the environment
Chemical: Chemoautotrophs or lithoautotrophs
H2S 2H+ +S +2e2NH3 + 4O2 2HNO3 + 2H2O
4FeCO3 + O2 + 6H2O 4Fe(OH)3 + 4CO2
or
Sunlight: Photoautotrophs
nCO2 + nH2O (CH2O) + nO2
Energy is needed to build and maintain structures
a) mechanical energy
b) chemical energy
c) osmotic energy
d) light energy
- muscles
- electric eel
- plant turger
-bioluminescence
4
3) Most characteristic attribute of living things is selfreplication and self assembly
it is the quintessence of the living state
1 single bacteria 109 in 24 hr
inanimate matter does not do this
also the near-perfect fidelity of this process is awesome!
A crystal at equilibrium grows but life at equilibrium is
death!
Life is a set of relationships characterizing the nature, function and
interaction of biomolecules.
5
Philosophers thought life contained a “vital force” or
vitalism but this has been rejected by modern science.
Important insights and practical applications in medicine,
agriculture, nutrition and industry have come from
Biochemistry but ultimately biochemistry is still concerned
with the
WONDER OF LIFE
A Brief History of Biochemistry
6
Early 19th Century
World made of either "living matter" (organic) or "non-living
matter" (inorganic).(Vitalism)
1828 Friedrich Wohler accomplished the synthesis of Urea from
inorganic matter.
1897 Edvard and Hans Buchner showed dead cell extracts can
perform reactions of living cells.
The molecules responsible for performing these reactions
are called enzymes
Late 1800's Emil Fischer suggested key/lock picture.
Substrate Key, Enzyme Lock
Early 1900's Field of biochemistry emerges
Structure and function of enzymes
Elucidating enzymatic pathways
1944 Genes composed of DNA
1953 Watson and Crick determine the structure of DNA
Biological function linked to the information in genes
Double helix slide
Phylogenetic Tree of Showing Three domains of Organisms
How did organisms evolve?
• Blind watchmaker principle, small
mutations arise at random.
1. Evolution is not directed
2. Evolution requires in-built sloppiness
3. Evolution is constrained by the past
4. Evolution is ongoing
10
CAN you name a few of the recent discoveries?
Range of Life- Hot springs -subduction zones -artic
tundra- Antarctic dry fields - from animal intestines to
college dormitories. These are all equal to specific
biochemical adaptations.
Is Life Unique to Earth?
Tools of the trade
3D models space filling or stick models
H - white
C - black
N - blue
O- red
P - yellow
S - yellow
•Stick or skeletal models show molecular frame work
but not atomic radii
•I suggest that you get a model set to help with
steriochemistry and structure.
Physical Units of Space, Time, and Energy.16
LENGTH You must know this and be comfortable using them.
Length is very important!!
•C - C bond is 1.54 Å
•Hemoglobin 65Å
•Ribosomes 300Å
•Viruses 100 - 1000Å
•Cells 7 m or 7 x 104 Å
1Å
10-10 m
10 Å
10-9 m
100 Å
10-8 m
1 mm = 10-3 m
1 m = 10-6 m
1 nm = 10-9 m
1000 Å
10-7 m
104 Å
10-6 m
105 Å
10-5 m
Limit of a light microscope = 2000 Å or 0.2m
1 Å 104 Å knowledge comes from X-ray crystallography, electron
microscope or atomic force microscope
Life is in constant flux
17
Enzyme catalyzed reactions- Substrates Products 10-3 sec - milli sec
Unwinding of DNA 10-6 sec - micro sec
10-15 s
femto
10-12 s
pico
•femto fs
•pico ps
•nano ns
•10-8 10 ns
•micro s
•milli ms
•103
•2.3 x 109 sec
10-9 s
nano
10-8 s
10-6 s 10-3 s 10 s 103s
micro milli sec
excitation of chlorophyll
charge separation in photosynthesis
hinge protein action
fluorescence lifetime
DNA unwind
enzymatic reactions
generation of bacteria
average human life span
Energy
Ultimate source of energy is the sun
E = h 57 Kcal/mol of photons green light
or
238 KJ/mol
1 cal = 4.184 joules
0.239 cal = 1 J
You must know how to convert between the two.
ATP energy carrier, for hydrolysis to ADP + Pi
= 7.3 kcal/mole or 30.5 KJ/mol
While vibrational energy infrared) = 0.6 kcal/mol or 2.5 KJ/mol
C - C bond = 83 Kcal/mol or 346 KJ/mol
the framework of a carbon skeleton is thermally stable
but
non-covalent bonds are only a few kcal/mol or
10-20 KJ/mole
18
19
Thermal
Noncovalent
1
ATP Green
bond
light
10
100
C-C glucose
bond
1000
Kcal/mol
KJ/mol
1
10
100
1000
Biomolecule shapes and interactions are mediated by 4 types
of non-covalent bonds.
These bonds are responsible for the overall shape and interaction among
biomolecules and can be modified by thermal energy.
Boil an egg, fry a steak or get a sunburn.
1)
Electrostatic interactions
by coulombs law F= kq1q2
r 2D
20
q are charges
r is radius
D = dielectric of the media, a shielding of charge.
And k =8.99 x109Jm/C2
D = 1 in a vacuum
D = 2-3 in grease
D = 80 in water
Responsible for ionic bonds, salt linkages or ion
pairs, optimal electrostatic attraction is 2.8Å
2)
Hydrogen bonds
O-H N
2.88 Å
N-H
O
3.04 Å
H bond donor or an H bond acceptor
N H
O C
3-7 kcal/mol or 12-28 kJ/mol
very strong angle dependence
21
.
3)
22
van der Waals attraction
Non-specific attractions 3-4 Å in distance (dipole-dipole attractions)
Contact Distance
H
C
N
O
S
P
Å
1.2
2.0
1.5
1.4
1.85
1.9
1.0 kcal/mol
4.1 kJ/mol
weak interactions
important when many atoms
come in contact
Can only happen if shapes of molecules match
Steric complementarity
23
•Occurs when large numbers of atoms are in contact
Specificity
When there is a large affinity for a unique molecule to bind to another
a) antibodies
b) enzyme substrate
c) restriction enzymes
Dielectric effect
hexane
benzene
diethyl ether
CHCl3
acetone
Ethanol
methanol
H2O
HCN
D
1.9
2.3
4.3
5.1
21.4
24
33
80
116
24
H2O is an excellent solvent and dissolves a large array of
polar molecules.
However, it also weakens ionic and hydrogen bonds
Therefore, biological systems sometimes exclude H2O to
form maximal strength bonds!!
4*
Hydrophobic interactions
25
Non-polar groups cluster together
G = H - TS
The most important parameter for determining a biomolecule’s shape.
.
Entropy order-disorder. Nature prefers to maximize entropy “maximum
disorder”.
How can structures form if they are unstable?
Are they unstable? Structures are driven by the nature
of water interactions