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

ENERGY

c. store

d. use

Living things can extract energy from the environment

Chemical: Chemoautotrophs or lithoautotrophs

H₂S  2H+ _{+S +2e}

-2NH3 + 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 - muscles b) chemical energy - electric eel c) osmotic energy - plant turger

d) light energy -bioluminescence

3) Most characteristic attribute of living things is

self-replication and self assembly

it is the quintessence of the living state

1 single bacteria



10

9

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.

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

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

How did organisms evolve?

• Blind watchmaker principle, small

mutations arise at random.

1. Evolution is not directed

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

Physical Units of Space, Time, and Energy

.

LENGTH You must know this and be comfortable using them.

Length is very important!!

•C - C bond is 1.54 Å 1 mm = 10-3 _m

•Hemoglobin 65Å 1 m = 10-6 m

•Ribosomes 300Å 1 nm = 10-9 m

•Viruses 100 - 1000Å •Cells 7 m or 7 x 104 _Å

1 Å 10 Å 100 Å 1000 Å 104 Å 105 Å

10-10 m 10-9 m 10-8 m 10-7 m 10-6 m 10-5 m

Limit of a light microscope = 2000 Å or 0.2m

1 Å  104 Å knowledge comes from X-ray crystallography, electron

microscope or atomic force microscope

Life is in constant flux

Enzyme catalyzed reactions- Substrates  Products 10-3 sec - milli sec

Unwinding of DNA 10-6 sec - micro sec

10-15 _{s 10}-12 _{s 10}-9 _{s 10}-8 _{s 10}-6 _{s 10}-3 _{s 10 s 10}3_s

femto pico nano micro milli sec •femto fs excitation of chlorophyll

•pico ps charge separation in photosynthesis •nano ns hinge protein action

•10-8 10 ns fluorescence lifetime

•micro s DNA unwind

•milli ms enzymatic reactions •103 _{generation of bacteria}

•2.3 x 109 _{sec 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

Thermal Noncovalent ATP Green C-C glucose

bond light bond

1 10 100 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 q are charges

r2D r is radius

D = dielectric of the media, a shielding of charge.

And k =8.99 x10

9

Jm/C

2

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 N-H O 2.88 Å 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

.

3)

van der Waals attraction

Non-specific attractions 3-4 Å in distance (dipole-dipole attractions)

Contact Distance Å

H 1.2 1.0 kcal/mol

C 2.0 4.1 kJ/mol

N 1.5 weak interactions

O 1.4 important when many atoms

S 1.85 come in contact

P 1.9

Can only happen if shapes of molecules match

Steric complementarity

•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 D

hexane 1.9

benzene 2.3

diethyl ether 4.3

CHCl₃ 5.1

acetone 21.4

Ethanol 24

methanol 33

H₂O 80

HCN 116

H

₂

O 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 H

₂

O to

form maximal strength bonds!!

4* Hydrophobic interactions

Non-polar groups cluster together



G =



H - T



S

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