BAHAN KULIAH BIOKIMIA POWER POINT BAGIAN 1 /BIOCHEMISTRY POWER POINT LECTURES PART 1 | Karya Tulis Ilmiah

BCHS 3304: General Biochemistry I, Section 07553 Spring 2003 1:00-2:30 PM Mon./Wed. AH 101

http://www.uh.edu/sibs/faculty/glegge

Instructor:

Glen B. Legge, Ph.D., Cambridge UK Phone: 713-743-8380

Fax: 713-743-2636

E-mail: glegge@uh.edu Office hours:

Mon. and Wed. (2:30-4:00 PM) or by appointment 353 SR2 (Science and Research Building 2)

SIBS program

• Monday Chat room on Webct: 8:00-10:00 PM Tuesday Workshop: 5:00-7:00 PM in 101 AH Wednesday Office Hours: 3:00-4:45 PM in

114 S Wednesday Workshop: 5:00-7:00 PM in 116 SR1

• Students must activate their webct accounts. • SIBS will not print out exam reviews

Molecules and Water

Molecules in life processes

C, H, O, N, P, and S all readily form covalent bonds.

Only 35 naturally occurring elements are found in life processes.

Earth’s Crust 47% O2, 28% Si, 7.9% Al, 4.5% Fe, and

3.5% Ca.

Carbon

• Carbon forms the basis of

life

• Carbon has a tremendous chemical

diversity

• can make 4 covalent bonds

• can link together in C-C bonds in

all sorts of flavors

Boron

•Symbol: B

•Atomic number: 5

•Atomic weight: 10.811 (7) g m r

Nitrogen

• Symbol: N

•Atomic number: 7

•Atomic weight: 14.0067 (2) g r

•Nitrogen has five valence electrons

Silicon and Phosphate

• Silicon has a large radius preventing good orbital overlap thus Si-Si bonds are relatively weaker at 177 kJ/mole

• This makes longer Si-Si chains are unstable • Si-O bonds are very stable 369 kJ/mole

• Si cannot have higher oxidation states other than SiO₂ which is sand

Carbon heteronuclear bonds

• Heteronuclear are stable and form in living matter

• These bonds are less stable than C-C bonds

Life developed from “carbon-based”

Self Replicating RNA molecules “RNA

World” Catalytic RNA.

Chemical Evolution

.

From HCN, NH₃, H₂O give rise to adenine or carbohydrates.

By sparking CH₄, NH₃, H₂O and H₂ these are formed:

Glycine glycolic acid Sarcosine Alanine Lactic acid N-Methalanine

-Amino-n-butyric acid  - Aminoisobutyric acid - Alanine

Valence orbitals: outermost orbital that is filled or partially filled with electrons. These can overlap and form covalent bonds.

Each orbital can have two electrons. Orbitals are designated by quantum numbers which define shells, orbital types spin etc.

electron or Val Max # 0f own val Bond Lone Element proton # orbital # electrons electrons # pairs H 1 1 2 1 1 0 C 6 4 8 4 4 0 N 7 4 8 5 3 1 O 8 4 8 6 2 2

Covalent bond: the force holding two atoms together by the sharing of a pair of electrons.

H + H  H:H or H-H

The force: Attraction between two positively charged nuclei and a pair of negatively charged electrons.

Orbital: a space where electrons move around.

Electron can act as a wave, with a frequency, and putting a

Molecules have a definite shape

C

O

B

A

O H HO H HO H OH OH H H OH

• A, B, C, and O all lie

in the same plane.

• As the molecule

becomes larger the

shape becomes more

complicated

• And may have many

different

C

CH

4

N

NH

3

H

2

O

O

Measurement of polarity

Dipole moment directionality: Vector from - to +

X

+

Polarity of Bonds

H

| + _

-CH

₃

OH H—C—OH C O

|

H

or even stronger polarity

H



+



-



+



C O C O

H

O> N> C, H electronegativity

- _+ _+ _- _+ _

Geometry also determines polarity

• 

+



-• while

C

Cl

is polar

carbon tetrachloride is

not. The sum of the

vectors equals zero

and it is therefore a

nonpolar molecule



CCl4

=



₁

+



₂

+



₃

+



₄

= 0

C

Cl

Cl

Cl

Cl

1 2 3 4

C

Cl

Cl

Cl

2 3 4

H

Properties of Water

Hydrogen bonds

Physical properties of ice and water are a result of

intermolecular hydrogen bonding

Heat of sublimation at 0

o

C is 46 kJ/mol yet only 6 kJ/mol is

gaseous kinetic energy and the heat of fusion of ice is 6 kJ/mol

which is only 15% of the energy needed to melt ice. Liquid

water is only 15% less hydrogen bonded than ice

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/mole or 12-28 kJ/mole

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

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

•Heat of sublimation of ice is 46.9 kJ/mol

•Only 6 kJ/mol can be attributed to Kinetic energy of the gaseous water vapor molecules.

41 kJ/mol must come from hydrogen bonds.

Only 15% of the hydrogen bonds are disrupted by melting

Short term interactions are tetrahydral in nature

Water reorients once in 10-12 _{sec that is a pico second}

Liquid water therefore consists of a rapidly fluctuating, -space filling network of hydrogen-bonded H₂O molecules that, over

Water of Hydration

• Hydration - to be surrounded by H

₂

O

• A polar molecule is hydrated by the partial

charge interaction of the water molecule

.

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

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

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?

Non-polar molecules are not soluble in H

₂

O

Tendency to associate with each other and to be excluded from water.

HYDROPHOBIC INTERACTIONS

Grease or gasoline does not mix with water.

However, small non-polar molecules like CH₄ (methane) have a small solubility. But when the water is evaporated, a solid remains

.

A calatherate is formed!!

STRUCTURED WATER

A cage of water molecules surrounding the non-polar molecule

This cage has more structure than the surrounding bulk media.

G = H -TS

Entropy decreases!! Not favorable! Nature needs to be more disorganized. A driving force.

SO

To minimize the structure of water the hydrophobic molecules

cluster together minimizing the surface area. Thus water is

Free energy of transfer for hydrocarbons

form water to organic solvent

CH₄ in H₂O  CH₄ in C₆H₆ 11.7 -22.6 -10.9

CH₄ in H₂O  CH₄ in CCl₄ 10.5 -22.6 -12.1

C₂H₆ in H₂O  C₂H₆ in C₆H₆ 9.2 -25.1 -15.9

Amphiphiles

• Most biological molecules contain both

polar

and

non-polar

segments

• They are at the same time

hydrophobic

and

Amphipiles: both polar and non-polar

Detergents, Fatty acids, lipid molecules

• polar head; non-polar tail.

• Water is more concentrated than the molecules it

surrounds so the shear numbers of ordered

molecules is much greater. The greatest entropy

is a function of both the dissolved molecule and

the solvent.

Amphiphiles form micelles, membrane

bilayes and vesicles

• A single amphiphile is surrounded by water, which forms structured “cage” water. To minimize the highly ordered state of water the amphiphile is forced into a structure to maximize entropy

Osmosis and diffusion

• Osmosis is the movement of solvent from aregion

of high concentration to low concentration

Proton and hydroxide mobility is large

compared to other ions

• H

3

O+ : 362.4 x 10

-5

cm

2

•V

-1

•s

-1

• Na

+

: 51.9 x 10

-5